What Dreams May Come
by Sequoia Hope
Summary: When Elizabeth is left behind on the Replicator planet, John is determined to go back for her. But the rescue mission doesn't go as planned, and when a shattering reality crashes down on him, John is forced to recognize a painful truth that he hadn't realized existed until now. Main story takes place between 4.03 Reunion and 4.04 Doppelganger.
1. Chapter 1

**What Dreams May Come  
** By Sequoia Hope

* * *

 _…To die, to sleep –  
To sleep, perchance to dream. Ay, there's the rub,  
For in that sleep of death what dreams may come,  
When we have shuffled off this mortal coil,  
Must give us pause… _(III.i.72-76)

– _Hamlet_ by William Shakespeare

* * *

 **Prologue**

"What about Elizabeth?" Though her voice was steady, Teyla's disquieted expression seemed to convey that she somehow already knew. John looked away, not responding. A long moment passed, and he felt Teyla wrapping her arms around him, her tears falling silently.

His own heart was going to painful, familiar places, but the city was still adrift in space, and he couldn't afford to lose his focus, not now. But that night, after the city had landed safely with power to spare, he was alone in his darkened quarters when the doorbell rang.

"Teyla?" John saw Teyla standing before him. She looked down, and he saw that she was holding something in her hand.

"I found this in her office. I thought that you should read it." Teyla's voice was quiet as she slowly offered him a torn white envelope. John looked at it apprehensively, then took it without a word. When he looked at Teyla, her eyes revealed a mixture of sorrow and empathy. She placed her hand on his arm gently, then left the room.

John closed the door, and after a brief moment of hesitation, he opened the envelope. He unfolded the single sheet of paper inside, and upon reading the enclosed words, he felt his heart breaking like a dam, and the water was rushing in uncontrollably. He stood up, breathing heavily, and the paper and envelope lay discarded on his bed as he paced back and forth, feeling emotions that he couldn't express about to burst out of control. The next thing he knew, he was staring down at a bloodied fist, and shards of glass lay strewn on the floor as a cold night wind swept in through a broken window.

 _The shattered pieces of glass came down like a crashing waterfall to the floor of her office, and he vaguely saw her holding her hand up and shouting to the security detail to stand down. He was losing himself, he felt his sense of self slowly drifting away as he later sat alone in his darkened quarters._

 _Later, she confronted him alone with the bad news. He saw the fear in her eyes, and her voice didn't sound whole, but she didn't break her gaze, nor did she step away from him. Even when he attacked her and she fought his grip, she looked straight into his eyes and didn't flinch. Then he woke up in the infirmary, and he heard her voice first. She walked with him to the Gate, remaining by his side every step of the way on the mission to save his life._

"God dammit," he whispered.

* * *

 **Chapter 1**

 _Nineteen days after Atlantis arrives on New Lantea_

John Sheppard sat on one side of a long table, and on the other side were three stoic faces, staring at him impassively. It was the first time that he found himself going head-to-head with the IOA. And he already hated these damn bureaucrats.

"With all due respect, Atlantis willingly cooperated in the Apollo's mission to nuke the Replicator ships, and in doing so, we saved your asses here on Earth." John tapped his fingers on the table, frustration building within him. "Earth's safety, however, came at the expense of Atlantis', because that strike provoked the Replicators to attack our city, and we ended up having to evacuate our planet. During the evacuation, many people were injured, including Dr. Weir, and we were also losing power. In a last-ditch attempt to survive, we were forced to steal a ZPM from the Replicator planet, and it was only with Dr. Weir's help that we escaped with our lives." He leaned forward, his voice unrelenting. "Elizabeth's the reason that you don't have to worry about creepy alien robots blasting this planet to bits right now, and she's the reason that we got off the Replicator planet and our people in Atlantis didn't turn blue in the vacuum of space. If you think that we're not going to try to go back for her after everything she did for us, then you're sorely mistaken."

"In your mission report, however, was it not stated that Dr. Weir sacrificed herself when you and your people attempted to upload the Wraith attack command code into the Replicator central data core, not when stealing the ZPM?" Ambassador Shen Xiaoyi interrogated, her eyes steely.

 _Crap._ "Yes, but –"

"It would appear that your team could have left very quickly after stealing the ZPM, with Dr. Weir, with no trouble at all from the Replicators," British Representative Russel Chapman interrupted. "Yet, your team chose to linger in order to complete a task that was not on the mission's original agenda. It sounds a bit reckless, considering your foremost priority at the time was to save your city and the people in it, was it not?"

"We were in a position where we could turn the Wraith and the Replicators against each other, and as we are sitting here discussing this, the Wraith and the Replicators are kicking each others' asses. We're saving thousands, if not millions of lives in that galaxy. We knew the risks involved –"

"– And you paid dearly for them." The Ambassador's eyes were cold and unsympathetic. "Colonel, it was your people who made a decision that led to her capture, and we fail to see how the IOA should be held accountable for Dr. Weir's loss. What is more, given that you have no viable plan, a rescue mission is out of the question."

"And we cannot forget that Dr. Weir is compromised, given that she is part Replicator," Dr. Natasha Morozov added in a heavy Russian accent. "If her nanites are able to connect to the Replicator collective, even if you were able to find her, she would be a security threat to the city."

"Elizabeth is able to control her nanites, and we can reprogram them to do only what we want," John said, his words not sounding so convincing.

"That is of great reassurance to us." Dr. Morozov retorted.

 _God, where's Woolsey when you need him?_ "Leaving her behind is also a security threat to the city. They'll probe her mind for intel, and the longer that we leave her there, the more information they'll be able to gather about us." His mind was in a frenzy. He was running out of arguments.

"But they don't know the current location of Atlantis," Representative Chapman countered. "If you return to the Replicator home world, and you are caught, the Replicators will be able to obtain more valuable information about Atlantis from you than they could with Dr. Weir. It is clearly of greater risk to the city to launch a rescue mission than it is to refrain from one."

"Colonel, you stated in your report that you were against Dr. McKay reactivating Dr. Weir's nanites for the very reasons that you are dismissing now," Ambassador Shen said, her tone accusatory. "It sounds reckless that you would now choose to risk the security of Atlantis merely for one person."

"Yet is it all that surprising?" Representative Chapman muttered. The Ambassador turned her head to glance at him briefly, then turned back to John, her eyes void of warmth.

"And all of this is based on the assumption that she is still alive."

A dead silence fell over the room. A long moment passed before John slowly placed his hands on the edge of the table. His knuckles tightened, and when he spoke, his voice was low and menacing.

"Let me make something very clear. To all of you. Elizabeth is still out there, and there is no way _in hell_ that we are leaving her behind. She is a member of my team, and with or without nanites, as far as I'm concerned, she is a live, human being who is now a prisoner of war." He rose slowly, trying to control his breathing. His eyes burned with inexpressible emotions. "We don't leave our people behind, and I will be damned if I don't get her back."

John shoved his chair away from the table and stormed out of the room, paying no attention to the looks of surprise and disapproval as he slammed the door behind him.

* * *

 _Four days later_

The control room was occupied by a handful of technicians and scientists as John walked across the bridge. He spotted Rodney McKay typing away furiously at his computer console, his face strained with intense concentration.

"How's it coming along, Rodney?" he asked as he approached.

"Still working on it," Rodney muttered, not looking away from the screen.

"Just wanted to let you know," John began, leaning against the console, "that the IOA finally gave me their decision. Their answer's no." Upon hearing this, Rodney looked up briefly, then turned back to the screen. John tapped his fingers, then leaned in closer to Rodney. "Look, I asked Carter over a week ago, and getting past her now is our only chance of getting Elizabeth back. I want a status update."

"'Working on it' is the status," Rodney retorted, glaring at John. "Look, there's just a lot of problems to work through, and I'm betting that there are a lot more that I haven't even thought of yet."

"Give me the deets," John demanded.

Rodney sighed loudly, shaking his head in impatience. "First, the Daedalus and the Apollo are both back in the Milky Way and are weeks away from Atlantis, so they can't help right now. Second, the place is going to be swarming with Replicators, and our ARGs definitely won't hold them off for long. How do you expect to search the city without getting captured?"

"Well, you've been working on a new freezing program, right?" John asked. "So can't you freeze them again?"

"The only way for me to do that is if I have direct access to the Replicators' base code or upload the program into a Replicator directly, and I highly doubt that we'll get any volunteers to temporarily turn them into statues," Rodney replied. "And not to mention that we have no idea where to begin looking for her."

"We start in the most likely places," John said. "Maybe the brig or their labs."

"Sheppard, our tracking devices have no way of distinguishing her from the other Replicators, and we have no way of communicating with her," Rodney argued. "You're talking about doing an extensive floor-by-floor search of the entire city. Do you realize how many hours, if not days, it would take to search the place?"

"Yes, Rodney, I'm well aware of that," John replied, his eyes narrowing.

"And that's assuming that the Replicators aren't on our tails trying to kill us at every moment." Rodney turned back to the computer console, his bleary eyes scanning the computer readings once more. "Look, I told you, I'm working on it, but there are so few options available right now, and I need more time."

"We don't have more time," John said, his voice tense.

"You think I don't know that?" Rodney burst out. He looked up at John, his red eyes reflecting exhaustion and frustration. "Look, every single day, I'm racking my brains out trying to figure out how to get her back. It's my fault that she's not here right now, because if I hadn't found that stupid code, we could have left right after we got the ZedPM instead of trying to save the entire galaxy like we usually do. And look where that got us this time." Rodney stopped abruptly, as if a sudden realization had just slapped him in the face. He looked away. "It's my fault that she's not here. I want to get her back, and it hurts so much that I'm stuck and can't figure out how."

John looked at Rodney's strained face, and he sensed that Rodney was in more pain that he was letting on. He sighed and looked down.

"All right," he said, his voice low. "Just keep me posted."

He turned around and began heading out of the control room.

"Sheppard." John stopped in his tracks. Slowly, he turned around to face Rodney again, who was avoiding his gaze.

"I hate to say it, but… what if she's compromised?" Rodney's voice was pained. "You know… what if she's one of them? Maybe… maybe we've already run out of time."

John looked at Rodney, feeling something that he couldn't express building inside of him. His hands clenched into fists, his knuckles tightened, and his eyes felt like they were about to shoot out of their sockets. Suddenly, he changed his mind, and he turned abruptly and headed for a different set of stairs.

"Sheppard?" Rodney sounded alarmed behind him. "Sheppard, where are you going?"

"I'm not waiting any longer," John said, heading up toward the Jumper Bay, taking the steps two at a time.

"What are you talking about?" Rodney sounded bewildered.

"I'm getting her back, Rodney, right now."

"What?! You can't be serious!"

"McKay, what's going on?" John heard Ronon's voice on the flight below him.

"Sheppard's going after Elizabeth," Rodney replied, sounding panicked. "Sheppard, wait!"

* * *

By the time the rest of his teammates caught up with him, John had already strapped on a tac vest and grabbed a couple of ARGs, and his mind was racing in anticipation of the next few hours.

"John, what are you doing?" Teyla demanded as she approached him in the Jumper pilot's seat.

"I'm going after Elizabeth," he replied, his attention on the HUD in front of him.

"Sheppard, are you insane?!" Rodney exclaimed. "You can't just stroll in there and expect that they'll greet you with wide open arms and turn Elizabeth over with a simple 'please' and 'thank you.'"

"Rodney has a point," Teyla spoke again, her voice firm. "Without a clear plan, how do you expect to find Elizabeth and escape the planet without being detected or captured by the Replicators? This is reckless, and not to mention, you have not cleared this with Colonel Carter."

"All I need is a couple of ARGs, a life signs detector, and some sheer damn luck," John replied, his voice flat. "I'll improvise as I go along. And to be honest, at this point, I don't really care what she says."

"Isn't your record tarnished enough?" Rodney rebuked.

"Not only is Colonel Carter our leader now, but she is also military," Teyla interrupted. "Whether or not you succeed, this unauthorized rescue mission could very well have severe repercussions on not only your record, John, but also your post here in Atlantis."

"You think that I don't know that?" He turned around slowly in his chair and looked around at his teammates, his eyes hardening. "Look, we've waited too long. The IOA was never going to approve, and I am now kicking myself for not having done this sooner." His voice was uncompromising. "I'm not waiting anymore to come up with a plan for a mission that has its risks one way or another."

"John, we cannot let you do this," Teyla insisted, grasping his shoulders firmly. "Yes, there will be risks, but to attempt a rescue without any sort of plan increases those risks drastically. If you can give Rodney more time –"

"We don't have more time!" John yelled, his eyes enraged. He felt Teyla's grip on him loosen slightly, and her expression turned surprised. He suddenly realized that he had shouted louder than he had intended, and he tried to get his breathing back under control. "And neither does Elizabeth."

"Oh, and I suppose you think you can single-handedly pull this off?" Rodney snapped back. "Who do you think you are, a one-man army against an entire armada of replicating robots?" John looked at him, and then at Teyla and Ronon. He clenched and unclenched his fists, his knuckles turning white.

"Look, you guys are welcome to join me if you want to, or you can stay behind. I'm not gonna blame you for doing so." He looked at his teammates with a fierce expression, as if daring them to challenge him again. "But regardless, I'm going after her." He watched as his teammates exchanged a few apprehensive glances with each other.

"What's Carter going to say when you come back?" Ronon asked, his voice matter-of-fact.

Upon hearing Ronon's words, John tore up the last shred of caution that had hampered him all this time from what he was about to do.

"I'll deal with the consequences once Elizabeth's back in Atlantis," he said, his voice darkly low. "I'm not coming back without her."

There was a moment of silence. Then Teyla lowered her head in resignation, and Ronon gave a small nod of acknowledgement.

"Well, we can't let you do this alone," Rodney said, sounding nervous.

John looked around at his teammates, their faces expressing conflict but determination. He nodded.

"Get your necessary equipment. We're going now."

There was a flurry of movement as his teammates hustled out of the Jumper to get tac vests and ARGs from the armory. John settled back in the pilot's chair, already feeling weary. But then his eyes hardened in determination again, and he kept his mind focused on the only one acceptable outcome of this mission.

"Dial the closest space gate to the Replicator planet," he instructed Rodney when his teammates returned, and he powered up the Jumper. "We'll cloak on the approach."

"On it," Rodney muttered. John looked out the windshield as the Jumper descended into the Gate Room. He caught a glance at Colonel Carter, looking surprised and shouting orders to Chuck, presumably to shut off the Gate and patch a radio signal through to the Jumper. But the Jumper was in control now, and he had deliberately shut off his radio beforehand.

 _"Arclight, this is Roundhouse Zero-Six. Do you read?" John's voice was tense, his mouth dry from lack of water, and he silently cursed the useless device._

 _"Sheppard… whatever happens, thanks for coming for me."_

 _John looked down at Holland, hearing the exhaustion in his voice, seeing signs of lost hope in his eyes. He looked up around him at the endless sand dunes, and his whole body was fatigued from all the running and the relentless dust and heat. His mind filled with visions of his crashed Apache helicopter, then the old Russian one in which he found Holland, who now lay beside him, saying things that made it seem like he believed he wasn't going to make it._

 _"Arclight, this is Roundhouse Zero-Six. Do you read? Arclight, this is Roundhouse Zero-Six. Do you read?" Even as he repeated those words like a broken record player, he began to realize that no help was coming, and he was alone with a comrade and friend who lay dying._

"All right," John breathed. "Let's do this." He commanded the Jumper to move forward, and they disappeared through the Gate.


	2. Chapter 2

**Chapter 2**

The Jumper exited the Gate, and John turned on the cloak. "All right, our ETA is two minutes. We should be –"

There was a sudden explosion outside the Jumper, and the ship lurched from the violent turbulence.

"What was that?" Teyla asked, sounding alarmed. The Jumper shook again as something impacted the outer hull.

"All right, we're switching from cloak to shields!" John mentally gave the order to the Jumper, then tried pressing a button, but nothing happened. "Rodney, the shields aren't working!" He looked out the windshield, an appalled expression forming on his face as a ship comprised of organic material, escorted by three smaller ships, came into the Jumper's view, firing weapons.

"Wraith cruisers," Ronon said. "And a Hive."

"Did they see us before we turned on the cloak?" Teyla asked.

"I sure as hell don't know," John replied, "and I'd rather not stay long enough to find out. We can't engage them with only one Jumper." He ducked his head as the Jumper took another hit. "Rodney, shields!"

"I heard you the first time!" Rodney retorted, furiously reading his computer tablet. "The mechanism that switches the Jumper from cloak to shield and vice versa has been damaged."

"What's that?" Ronon asked, viewing in a different direction out the windshield. Another ship, this one different in aesthetic and technological design, was approaching them and also firing weapons.

"You've got to be kidding me!" John exclaimed.

"Wait." Rodney stepped forward, his eyes flickering back and forth between the two ships, watching their weapons flying through dark space. "I don't think the Wraith are attacking us." He watched the second ship as it came into view, and he looked at John with a surprised expression. "That's Ancient technology," he said, pointing to the second ship. "I'll bet you anything that that's a Replicator warship. I think that we've just found ourselves in the middle of a Wraith-Replicator battle."

"Well, Rodney, that's slightly more comforting to know that the Wraith and the Replicators are kicking each others' asses and not ours," John replied, his face contorted as he struggled to fly the Jumper. "But if you don't get those shields up, we're about to become casualties of war." He commanded the Jumper to dodge the weapons coming at them in opposite directions, then suddenly lurched forward, and he threw his arms in front of his face to avoid impact with the front controls.

"Inertial dampeners have been hit, and so have weapons. I am keenly aware of the perilous situation that we are in, thank you for stating the obvious!" Rodney snapped back.

"If we do not have our shield or weapons, then we are already at a disadvantage when we arrive at the planet," Teyla indicated.

"I'll be damned if this crossfire thwarts this mission before it's even begun," John replied, his brow furrowing in concentration as he continued to dodge the weapons, though it was becoming more difficult to steer the Jumper with the physical effects of inertia now more noticeable.

"The Jumper has taken on severe damage," Rodney said, his voice tense. "We need to get out of this now."

"All right, guys," John said, his eyes narrowing. "Now's your chance to see what it's like to be the alien ship in Galaga. Hang on!"

The Jumper flew up and down, swerved from side to side to avoid the relentlessly endless stream of weapons fire. At one point, John just barely sandwiched the Jumper between two energy blasts from opposite directions before propelling the Jumper upward at a sharp ninety-degree angle to avoid impact with another weapon coming directly at the windshield.

"That was a close one," he said, a little breathless.

As the words came out of his mouth, a powerful blast impacted the left side of the Jumper. John felt himself thrown out of his seat, and he wasn't sure if he hit his head or not. He attempted to get back up, but the g's were now taking an incredible toll on him. His mind couldn't concentrate, and the last thing he saw was the bright weapons fire out the windshield before everything went black.

* * *

There was a sharp pounding in his head. John twitched slightly, then slowly lifted his eyelids, squinting at the bright light.

"John?" There was the sound of movement, and Teyla appeared beside him. He realized that he was lying on the floor of the Jumper.

"What happened?" he groaned, trying to get up, then falling back on his backside as his head pounded like a heartbeat.

"I saved your sorry asses, that's what happened." Rodney's griping voice came from the front of the Jumper.

"You were thrown out of your seat and fell unconscious," Teyla explained, her voice gentle. "It appears that attempting to control the Jumper while under the physical effects of damaged inertial dampeners was more difficult for you than expected. Rodney managed to take control of the Jumper and fly us out of the crossfire and to the Replicator planet."

"So we're here?" John asked.

"Yes, we are," Teyla replied with a smile. She observed him closely. "How are you feeling?"

"Aside from my head feeling like it's been split in two?" John grimaced. "And how long have I been out?"

"Only approximately twenty minutes," Teyla replied. "It does not look like you have any apparent injuries. Do you feel well enough to proceed with this mission?"

"You know, I haven't heard a 'thank you' yet for my act of bravery that saved all of your lives!" Rodney complained.

"Thank you, Rodney!" John called out, his tone half sincere. "Looks like I've trained you well." He turned back to Teyla. "Just get me some Tylenol, I'll be fine. How about you, are all of you all right?"

"We are fine," Teyla said, smiling. "The damage to the inertial dampeners was actually not quite as serious as Rodney had initially anticipated. He has also been working on repairs for the mechanism that switches cloak from shield as well as weapons."

"The cloak is still operational, thank God," Rodney grumbled. "We haven't been detected – not yet, at least."

"Let's keep it that way," John replied. "Hopefully, with that battle going on up there, the Replicators are too occupied at the moment to deal with us. This should make things a lot easier. Here, help me up." He grabbed Teyla's extended hand and slowly got to his feet. He then stumbled to the rear compartment, where Ronon was waiting, and dug around for the first aid kit.

"You feeling all right?" Ronon asked.

"Yeah, I'm ok," John said, opening a black metal box, his head still pounding. "Though I can't believe I passed out like that at the controls. Never happened to me before."

"First time for everything," Ronon said. John popped two pills into his mouth and took a swig of water.

"All right." He wiped his mouth with the back of his hand. "Let's get moving." He opened the door and exited the Jumper, the rest of his team coming after him.

"According to these readings, no Replicators are nearby," Rodney reported as he studied the life signs detector. He pointed to a circular metal door on the ground near them. "We'll get in through that metal hatch. We're on the roof of a building south of the central tower."

"All right." John mentally formed a plan. "We'll split up into teams of two. Ronon, you're with Teyla, Rodney, you're with me. We'll check out the most likely places where they might be keeping her first. Rodney and I will head down to the brig and look around the lower levels of the city. Teyla, you and Ronon cover the upper levels and search any labs you come across. She'll probably be kept in an isolated section of the city. Only engage the Replicators if they're in groups of four or fewer; otherwise, avoid them. We don't want to confront too many at once and have any escape, otherwise, it won't be long before they all know we're here. Rodney, put your freezing program on stand-by in case we have an opportunity to use it. Radio contact every half hour. Questions?" When no one spoke up, he handed Teyla a second life signs detector. "Let's go."

The team split up after descending the hatch. Teyla and Ronon headed down the hallway, and John and Rodney headed for the nearest transporter to get down to the brig.

"We should consider ourselves lucky that that Wraith-Replicator battle is going on right now as it is," Rodney muttered as they exited the transporter, then headed down a nearby stairwell, the surrounding hallways completely empty. "If not, we'd be ducking our heads at every corner by now trying not to get shot."

"Yeah, well, let's hope our luck stays that way," John said, turning a corner.

"Wait." Rodney stopped walking, and John turned around to see him reading his detector. "The brig is around that way," Rodney said, jerking his thumb to the left, "and I am reading two life signs at the entrance."

"All right, let's see what we're up against." John continued down the hallway toward a corner, his footsteps quick and silent as Rodney followed him. He peered around the corner toward the entrance to the brig, and he glimpsed two Replicators in their habitual off-white attire stationed on opposite sides of a door.

"You got the one on the right," he whispered to Rodney. As he spoke, he heard footsteps approaching from an adjoining hallway, and he pressed his back against the wall.

"Your help is requested in the control tower." John heard a deep male voice echoing in the hallway.

"Of course," a different voice replied. He heard footsteps now approaching his and Rodney's position, and he signaled to Rodney to fall back. The two of them crouched in the shadows of the stairwell from which they had descended, and John watched as a Replicator with black hair and a tightly set jaw went up the staircase, not noticing his and Rodney's presence. The Replicator's footsteps faded away, and John emerged from his position and approached the nearby hallway once more.

"There's only one life sign reading now at the entrance," Rodney confirmed. John peered around the corner again, then without hesitation, he raised his ARG and fired at the lone Replicator standing at the door. The energy beam hit him squarely in the chest, and he disintegrated and fell to the ground like sand. He ran down the hallway, and he ignored the crunching sounds below his feet as he opened the door.

The brig was empty.

"All right," John said, realizing that the search was going to take a while. "Let's keep looking."

* * *

"Teyla, this is Sheppard. How are you and Ronon doing?" John spoke into his radio twenty minutes later.

 _"Colonel, Ronon and I are in the eastern section of the city,"_ Teyla replied. _"We have searched four levels in this section, yet we have not found anything."_

"Yeah, well, same goes for me and Rodney," John replied, frowning. "Have you come across any Replicators?"

 _"Only a few. Ronon and I have managed to either avoid them or dispose of them without complications. However, we feel that it is ineffective to perform a blind search of the city as we are doing now. Is it possible for us to narrow down the search parameters further?"_

"Rodney's coming up with a plan right now," John said, looking at the man in question.

"We need to get to the control room for two reasons," Rodney began. "One, I can access the Replicators' base code and upload the freezing program there. Two, once the Replicators are frozen, we can use the city-wide sensors to determine where they're keeping Elizabeth. Her reading will come up different because she's part human –"

"She _is_ human, Rodney," John cut in.

"Yeah, but she has active nanites as well, which means –"

"She's _human,_ " John insisted, his tone discouraging further dispute. "And get to the point."

"She's comprised of 97.1249 percent organic material," Rodney said, rolling his eyes. "So her reading will be different because she's not a machine. We'll be able to pinpoint her location in the city just like that."

"There's only one problem," John said, glancing above him warily. "The control room is occupied by Replicators. We're underneath the stairs leading up there now, and there are more than a handful of them. We need you and Ronon to come over and help us take them out."

 _"Very well. Ronon and I will arrive at your location shortly."_

"Sheppard out." John tapped his earpiece to break radio contact.

"I'm just saying, she has miniature robots keeping her alive –"

"McKay!" John shot Rodney a furious look, and Rodney backed down, grumbling incoherently.

A few minutes later, there was the sound of footsteps from down the hallway, sounding quick and urgent, and John emerged from his position as Teyla and Ronon rounded the corner.

"How many are there?" Teyla asked.

"I counted eleven," John grimaced. "Hopefully, no more have arrived." He suddenly heard the sound of approaching footsteps from above him, and he quickly motioned to his teammates to keep quiet. As he crouched back into the shadows, two pairs of feet appeared through the slats of steps, and John saw two Replicators coming down, one of them the black-haired Replicator that he had seen earlier. Then the Replicators disappeared down the hallway, their footsteps fading away.

"Make that nine, now," John said, slowly rising from his position.

"All right," Ronon said, sounding satisfied as he twirled his gun around in his hand, and there was a familiar _swoosh_ sound as he changed the gun setting. "Let's go kill some Replicators."

John silently led his teammates up the staircase, then peered into the control room. He then glanced behind him and motioned with his hand to signify their tactical strategy. Then he turned back to face the control room and rose from his position. Within a few seconds, all nine Replicators in the control room had crumbled to the floor like sand.

"All right, Rodney, get that freezing program plugged in," John ordered, heading toward the control consoles. "If other Replicators try to contact the control room, they'll know something's up when no one's responding. I'll check the city-wide sensors."

"How many more Replicators are in the city?" Teyla asked.

"Hopefully, few enough that we can handle them," John replied, his brow furrowing in concentration as he pressed a few buttons on the screen before him. "Once Rodney gets the freezing program up and we pinpoint Elizabeth's location, we're gonna swoop in to get her and leave. Should be a cakewalk."

"All right, freezing program is uploaded," Rodney announced. "Their code has been tampered with on an even more complicated level this time, so we should have more time than last time before they unfreeze and all hell breaks loose."

"Exactly how much more time is that?" John asked, studying the city-wide sensors, his voice not sounding so trusting.

"Oh, uh, approximately two minutes, thirty-eight seconds, give or take," Rodney flipped back.

"That's great, tell me the next time you have good news to share," John replied, slightly irritated.

"Oh, and I suppose that you think that you understand the absurd complexity of the Replicator base code better than I do –"

"This can't be right," John cut Rodney off, his eyes surveying the dots on the large screen before him, feeling a cold chill running through him.

"What, what's wrong?" Rodney stepped forward, looking at the screen as well, then his eyes widened as if in realization of their new problem. "She's not on here."

* * *

"Ok, we need to act fast." Rodney's voice sounded more agitated now. "There are a couple reasons for why she's not showing up on the city-wide sensors. She could be in one of the shielded sections of the city, or maybe the sensors simply can't identify her from the other Replicators because she's partially one of them."

"I thought you said that her reading would be different because –" John began, sounding irked.

"Yeah, well, so much for 97.1249 percent organic, huh?" Rodney muttered.

"This is all assuming that she's still here in this city, right?" Ronon spoke up.

"We're not there yet," John growled.

"I'm not saying that the Replicators killed her," Ronon explained. "I'm just saying that they might have taken her somewhere else, maybe off this planet."

"Ronon's right, she's too valuable for the Replicators to get rid of her," Rodney agreed. "I mean, with all the information she has on Atlantis –"

"Assuming that Elizabeth is here in this city on this planet," Teyla interjected, "where else could we look?"

There was a moment of uneasy silence. Then Rodney began snapping his fingers, his eyes lighting up as they always did whenever an idea suddenly occurred to him.

"The stasis chambers," he said, a look of disbelief on his face. "She's not in the brig, and I highly doubt that the Replicators would just leave her fully conscious in a room by herself, especially with the Wraith-Replicator war going on right now. No, they'd keep her somewhere safe in case they ever needed her, but she's otherwise stowed away so she doesn't cause them any trouble."

"To them, she's like a messy file cabinet," John said. "Full of valuable intel, but you only open it when necessary and shove it back in when you're done."

"Exactly," Rodney replied, turning back to the screen and pointing to two nearby locations. "The closest stasis chambers are here and here. If she's not in either of those places, then we'll try these two locations," he finished, pointing to two other rooms in the city.

"Sounds like a plan," John said. "Teyla, you and Ronon check out the ones on the northern side of the city, Rodney and I will get the ones in the east and south."

"We'd better hurry, the Replicators aren't going to stay frozen forever," Rodney said, sounding a bit apprehensive.

"You don't have to mention it, we already know," John muttered under his breath as he headed out of the control room.

A minute later, John and Rodney arrived at their first stasis chamber. John swiped open the door, and he looked around the darkened room. There were three chambers, and all of them were empty.

"Teyla, this is Sheppard," John said, tapping his earpiece. "How's it going on your end?"

 _"Colonel, Ronon and I have arrived at our first location, and Elizabeth is not here. We are on our way to our second location."_

"Same goes for me and Rodney," John replied. "We're heading to the one on the southern edge of the city."

 _"Very well. Good luck."_

"Sheppard out." He turned off his radio and headed down the hallway again.

John and Rodney soon arrived at their second location. Once again, John swiped his hand across the door control crystals, and he entered the darkened room, walking around slowly in what appeared to be an abandoned lab. He turned a corner, and he stopped when he noticed what was immediately across from him. There were three stasis chambers. All empty.

"Teyla, what's your status?" John whispered into his radio, his heart pounding.

There was a brief moment of radio static before there was a reply.

 _"Colonel, Ronon and I have thoroughly searched our second location, and Elizabeth is not here."_

John felt his mind begin to whirl uneasily.

"Copy that," he managed to say. He turned to Rodney, who was looking at him with a fearful, wide-eyed gaze.

"We're almost out of time," Rodney said, sounding distressed. "The Replicators are going to unfreeze any minute now."

"Are there any more rooms like this in the city?" John demanded.

"Not that I know of," Rodney replied, his voice frantic. "Maybe there are, but there are parts of Atlantis that we haven't even discovered yet, and it's possible that –"

"We don't have time for this," John cut Rodney off, clenching and unclenching his fists, his knuckles turning white. His head felt like it was about to implode, and he hit his fist against the wall. "We need to –"

His hand came in contact with a raised surface on the wall, and there was a _click_ followed by a muffled _swoosh_. John stopped talking, and he saw that he had hit a switch on the wall. He turned around behind him.

"What was that?" Rodney whispered, his eyes flickering nervously across the room.

John signaled Rodney to keep quiet, and he took a few silent steps forward. There was a door in the room that he hadn't noticed earlier, and he was pretty sure that the second noise had come from that direction. He raised his ARG with one hand, then threw open the door with the other, the light from his weapon dashing across the pitch-black room. The light fell on an empty stasis chamber. Then he directed the light toward the floor, and he felt his breath catch.

"Teyla. Ronon." John tapped his earpiece, and he had to make a conscious effort to get words out. "We found her."


	3. Chapter 3

**Chapter 3**

By the time Teyla and Ronon arrived, John was seeing signs of consciousness returning to the figure lying on the floor before him.

"Elizabeth?" John's voice was surprisingly quiet and low. Elizabeth stirred slightly, and her eyes flickered open.

"John?" She blinked in confusion, then looked around at the rest of the faces surrounding her. "Rodney?" She was gaping at them in shock. "Wh – What's going on? Atlantis – is the city safe? Did you make it to the new planet –"

"Hey, take it easy, don't worry," John assured her, placing a hand on her shoulder. "The city is fine, we got to the new planet."

"After we landed and settled affairs with the IOA and Stargate Command, Colonel Sheppard insisted on coming back for you," Teyla said, her voice gentle.

Elizabeth squinted at them. "The IOA authorized this mission?" she asked, her voice incredulous. There was an uncomfortable silence as the team exchanged a few apprehensive glances with each other.

"Um, well, not exactly," Rodney mumbled, his expression nervous. "Sheppard here – he, uh – he kind of did this on his own." Elizabeth slowly turned to John, her expression suddenly serious.

"Colonel, explain yourself." Her voice was humorless. "What's going on?" There was a moment of silence before John relented.

"The IOA was taking too long to reach a decision, and they were never gonna approve of this mission in the first place. And Carter wasn't going to let us go because McKay was taking too long to come up with a plan –"

"Colonel Carter?" Elizabeth interrupted.

"Um, yeah, Sam's the new you," Rodney said after a brief moment of silence, his voice meek. "Atlantis' new leader, I mean."

Elizabeth turned back to John, and he saw that her expression was deadly serious. "Colonel, you're telling me that you went against orders from your military superior on an unauthorized mission that could potentially endanger Atlantis and everyone in it?"

"Well, I think that that's a bit of an overstatement, considering that the Replicators are fighting it out with the Wraith now and have no idea where we are in the galaxy –"

"No, John, you listen to me," Elizabeth interjected, looking squarely at John. "Did it ever occur to you that the IOA and Stargate Command probably had good reason not to sanction this mission? You are risking the safety of Atlantis and our people, and I am clearly compromised and a threat to the city."

"Look, I knew the risks, and I wasn't going to let them stop me –"

"John, it was a mistake for you to come back here. All of you." Elizabeth said, looking at John, then up behind him toward the rest of his team. "The Replicators have tampered with my nanites, and I am not safe to be around anymore."

"We'll take you back to Atlantis," John said, trying to keep his voice under control. "We'll put you in an isolation room, and Rodney will figure out how to program them so they can't control you or the other Replicators while still keeping you alive –"

"No, it's too dangerous." Elizabeth's eyes were wide with frustration and fear. "The Replicators can take control of me at any given moment, and I will not risk Atlantis and the lives of everyone in it!"

"We'll figure something out, we always do," John said in a low voice, his eyes narrowing. "You're coming with us, we're not leaving you behind. We already did it once, and we're not doing it again."

"No, John, I'm not going." Elizabeth stared at him directly in the face, her expression resolute. "This mission was reckless, and you know it. You and your team need to leave now." She suddenly stopped talking, and her expression changed as if she was seeing something that the others couldn't. "You need to go now," she repeated, her voice carrying a sense of urgency this time.

"Not without you," John insisted.

"You don't understand," Elizabeth said, turning back to him with a wide-eyed expression. "It's the Replicators. They've unfrozen."

* * *

"The Replicators are on the move," Rodney announced, reading the life-signs detector. "I'm picking up two life signs about fifty meters down the hallway, and they're headed straight toward us."

"Go," Elizabeth said, getting up. "I'll go distract them. They won't be expecting me." John suddenly reached out and grabbed her arm.

"We can take them," he said in a low voice, and Elizabeth looked up at him.

"Go," she repeated, this time more firmly. "More are coming. I'll find you and your team later." Without another word, she broke free of his grasp and ran out of the room.

"She's right," Rodney said, still looking at the detector. "Six more are coming from the other direction." John turned back to his teammates.

"We need a new plan," he said, frowning. "We need to freeze those Replicators again so we can get Elizabeth and get out of here."

"Well, there's no time for me to go through the Replicator base code now," Rodney protested. "And Elizabeth's gone, so I can't do it through her –"

"Figure it out," John cut Rodney off. "We're not leaving without –"

"I am sensing something," Teyla interrupted, and John saw her expression turn unsettled.

Suddenly, there were noises echoing in the distant hallway. John heard what sounded like snarling, and there was a voice giving out shouts and panicked yelling.

"Elizabeth," he breathed. He bolted out the door, sprinting down the empty hallway, approaching the corner from where he was hearing sounds of struggle. He turned the corner, and what he saw nearly stopped him from breathing. Instinctively, he pulled out his 9 mil and began firing, cursing himself for not having a P-90, knowing that his pistol wouldn't have much of an impact on the Wraith pinning Elizabeth against the wall, its feeding hand raised in position, ready to feast on its prey. The Wraith looked up, its face covered by an armored mask, and it released its hold on Elizabeth. Out of the corner of his eye, John saw her drop to the ground, gasping violently for air, and her eyes and face were laced with horror.

He felt himself being thrown off his feet and flung through the air. His body hit a wall, and he fell like a rag doll to the ground. He heard a sharp ringing in his head, and he wrestled to get up on all fours, seeing his pistol lying on the ground a few feet away from him. John reached for his weapon, only to have his hand nearly crushed by a Wraith looming over him.

"If it makes you feel any better, you probably would have gotten infected if you tried to feed on her," he rasped. The Wraith grabbed his shirt and forced him to his feet, and he tried to turn away from the pungent odor coming from underneath the Wraith's mask. He recoiled slightly as it raised its feeding arm – and suddenly, he heard a blast of energy, and the Wraith dropped to the ground. He looked up in time to see a second Wraith meet the same fate as the first, and he saw Ronon running toward him, swinging around his weapon, with Teyla and Rodney close on his heels.

"You all right?" Ronon asked, a little breathless.

"Yeah, I'm fine," John responded, breathing heavily, his head still ringing.

"John?" Elizabeth's horrified voice rang through the air, and he looked up to see her frightened eyes locked in the direction down the hallway. There were six Wraith, all wearing masks and armor and carrying stunners, marching down the hallway toward them.

"Run," he heard himself saying. He reached for his pistol and forced himself to his feet, and he went to pull Elizabeth up. "Run, go, go!" he shouted to his teammates. They all bolted down the hallway, dodging energy blasts from the Wraith stunners, and he heard Ronon covering their six with his weapon. Then he suddenly stopped, a group of Replicators heading in their direction. "Oh, crap."

"Wait," Rodney exclaimed, and John looked at him with an incredulous expression. "They shouldn't attack us," Rodney said, his eyes wide. John watched in disbelief as the Replicators passed by him and his team as if they were no more than wallpaper and proceeded to fight the group of Wraith not too far behind them.

"Let's go," he breathed, and he and his teammates continued running through the corridors. As they distanced themselves from their attackers, his heart beat as if it were racing against time, and his mind whirled upon realizing that their situation had just become a lot more complicated. Eventually, he stopped in a secluded hallway, and he heard his teammates' footsteps slow down behind him.

"Everyone all right?" John asked, breathing hard.

"Oh, yeah, just great," Rodney wheezed, "with me having high enough blood pressure as it is." He stopped for a moment, clearly out of breath. "The Wraith – they must have somehow managed to infiltrate the city," he stammered, "especially if the Replicators were frozen up in that space battle, then the Wraith could have destroyed them and…"

"Great," John replied, taking deep breaths. "So now, we have not one, but two bad guys in this city who seriously want to kick our asses. But at least the Replicators are programmed to go after the Wraith when they're around." He turned to look at Elizabeth, whose hair was disheveled, and she still appeared breathless.

"Elizabeth? You all right?" he asked, his expression concerned. Elizabeth turned to look at him, and he saw that her eyes and face were still in shock.

"Yeah. I'm fine, I just –" Elizabeth stammered, seeming to struggle to get words out. John looked at her fearful eyes, and he took her hand and squeezed it.

"You'll be ok," he said in a quiet voice. Elizabeth looked up at him, and after a moment, she gave a small nod.

"We need to head back to the Jumper," John said, turning to the rest of his teammates. "We don't know how many Wraith are in the city, and seeing as the Replicators are now on the loose, they're probably going to call for reinforcements."

"John, I –" Elizabeth began.

"You're coming with us," John cut Elizabeth off, his expression stern. "If you think that we're going to leave you here right now with the Wraith lurking around at every corner, you're sorely mistaken." Elizabeth looked as if she wanted to protest his words, but still clearly rattled from the trauma, she looked as if she couldn't bring herself to argue with him.

"All right," John said. "Let's get moving."

* * *

"I thought you had Replicator spidey sense to know exactly where each of them are, so how come you didn't know that it wasn't Replicators back in the hallway where we were just now?" Rodney was talking with Elizabeth as John led the team down the hallway.

"Like I said, the Replicators tampered with my nanites," Elizabeth explained, sounding calmer now. "I thought it was them who were coming, but I guess I was mistaken."

"Crap." Rodney stopped in his tracks, his eyes widening as he studied the life signs detector. "I'm reading multiple life signs coming from both directions," he said, jerking his thumb down the hallway in one direction and then pointing in the other.

"We need to split up," John said, trying to think of options. There was a small hallway adjacent to theirs just up ahead, and the team ducked into its shadows.

"Teyla, Rodney, Ronon, you go down that way." John motioned further down the corridor. "Elizabeth, you're with me. We'll meet at the hatch that we entered from and go from there." He watched as half his team hurried down the dim hallway, then turned to Elizabeth beside him.

"We'll take cover here until they pass." John motioned to a shrouded corner, and he and Elizabeth ducked into the shadows, cowering in the darkness. He held his breath as the sound of marching footsteps approached them from two directions, and nearly a dozen Replicators entered their hallway.

"They are around here, I am certain." John saw the black-haired Replicator again among those in the hallway, and he shrunk further into the shadows to avoid being noticed. He felt Elizabeth pressing close to him, and he sensed that she was trying to keep her breathing calm. "We will try this direction," the Replicator spoke again, and John watched as he led the others down the corridor. The sound of their marching faded, then disappeared into silence. He slowly emerged from his position.

"All right, let's keep moving," John said. "We got to meet the others." He turned around and glanced down at Elizabeth, and he saw that her expression was humorless.

"John, this is a bad idea," Elizabeth whispered. "I can't go back, not like this."

"Look, I told you, it'll be fine," John insisted.

"No, John, you can't know that." Elizabeth's expression was laced with trepidation. "As I was sitting here with you just now, I was trying very hard not to imagine what might have happened if they had suddenly tried to connect with and take control of me."

"The fact that they haven't taken control of you yet says something, I think," John replied, trying to sound less grim. "You said so yourself that you were able to exert control over your nanites and prevent them from communicating with the Replicators."

"That was before they tampered with them." Elizabeth looked down at her hands, her expression sober. "I don't know what they did to me." John looked down at her despondent expression, then knelt down beside her.

"Look," he began, feeling a bit uncomfortable. "You remember when I nearly turned into a bug?" He watched as Elizabeth looked up at him in surprise.

"Never thought that I'd hear you bring up the subject yourself," Elizabeth replied.

"Yeah, I know," John grimaced. "Not exactly one of my yearbook moments." Elizabeth gave a small smile. "But the point is, you didn't give up on me, not even when I was… you know. And I'm not about to give up on you now." He watched as Elizabeth turned to him, her expression changing slightly, and for a brief moment, he thought he saw gratitude in her eyes. But if there had been a flicker of hope, it was quickly extinguished as Elizabeth turned away again.

"This is different, John," she said, her expression remorse once more. "That time, it was your life that was in danger. If I go back, it will be the lives of everyone in Atlantis."

"Two men were killed trying to save my life," John argued. "I'm not about to live mine without doing the same for others. It's a principle, Elizabeth. We don't leave our people behind."

Elizabeth shook her head. "I'm sorry, John. It's too great of a risk to take." John felt a sense of frustration and impatience building up inside him.

"Look, we came all this way for you, and you're right, it was against orders," he said, his eyes narrowing. "But you should know by now that this is what I do, Elizabeth. You knew that before we came here. And I know that… you trusted me then."

Elizabeth turned to him, looking confused for a moment, then her eyes widened as if she suddenly realized something. "How did you –"

"Teyla found your letter. And I read it."

Elizabeth looked away, her expression somber. "You should know that I trusted you to do the right thing the last time you were on this planet," she said, her voice quiet. John looked away.

"I did what I had to do." He tried to suppress the emotion building in his throat. "But it wasn't the right thing."

Elizabeth looked at him, and her gaze was saddened. "John, when have we ever played by the rules of right and wrong in this galaxy?" she asked, her voice carrying a sense of helplessness. John looked into her eyes, and he couldn't respond. Then he heard radio static in his headset.

 _"Colonel Sheppard, this is Teyla."_

He tapped his radio. "Teyla, what's your status?"

 _"Colonel, we were ambushed by the Wraith. They have taken Rodney."_

John looked at Elizabeth, whose expression was now alarmed, and he cursed silently. "Copy that," he managed to say. "What's your position, Elizabeth and I will meet you there."

 _"Ronon and I are at the transporter nearest the hatch from which we came in."_

"Copy that. Sheppard out." He turned off his radio, then looked down at Elizabeth, who was looking at him expectedly. He suddenly reached down and pulled her up.

"Come on, let's go." Without waiting for her to respond, he grabbed her hand and ran down the hallway, pulling her along beside him.

* * *

"We believe that the Wraith headed in that direction," Teyla said when John arrived with Elizabeth, motioning down the hallway.

"How many were there, and why didn't they take you and Ronon?" John asked, a little breathless.

"There were many, and I do not know," Teyla replied. "But they did not appear to want to feed on him, and they seemed particularly interested in Rodney because he did not appear to be military."

"Just great," John groused. "When I'm with a Wraith, I'm their food, but when McKay gets captured, he's somehow an asset." He exhaled sharply. "Ok, let's go see what these bastards want with our scientist of the week."

As he led his teammates down the endless corridors, nothing appeared on the life signs detector other than his and his teammates' dots. With every new corner they turned, John felt the pressure of time even more intensely, and he forced himself to suppress the apprehension building inside him.

"Maybe they took him aboard their ship," Ronon spoke up.

"Maybe," John replied in a low voice, half speaking to himself, "but we're not there yet." As he spoke those words, he looked down at his detector, and he saw that five dots had appeared on the edge of the screen. "This way," he said, taking off at a run, and he heard his teammates' pounding footsteps close behind him.

He heard muffled yelling behind a door at the end of a hallway. He signaled to Ronon to prep his weapon and nodded to Ronon and Teyla, then glanced behind him at Elizabeth, who was watching with fearful eyes. He gripped his pistol with one hand, and he threw the door open. Rodney was gagged and tied to a chair in the middle of the room, surrounded by four Wraith. These ones were not wearing armored masks.

"Let him go," John ordered, his pistol pointed at the Wraith.

One Wraith turned toward him, tilting his head as if questioning his statement.

"Or what?" it asked in a cold voice.

"Or we'll kill you," John replied, narrowing his eyes.

"Sheppard, I can take them," Ronon growled, his mouth curved as he aimed his own weapon.

"We will release Dr. McKay once he does exactly as we say," the Wraith said, his tone uncompromising.

"What do you want Rodney to do?" John demanded.

"To reprogram the Replicators' base code and remove the Wraith attack command code."

 _Dammit._ "And why would he do that?" John gripped his weapon more tightly.

"If he does not, then you will not get off this planet alive," the Wraith threatened. "Our ship is still in orbit, and we have detonators planted in the city, and we intend to destroy it."

"Well, if you were gonna destroy the city and all the Replicators in it anyway, what difference does it make if we remove that attack command?" John asked.

"Don't play fool with us!" the Wraith accused, its tone sharp. "The Replicator ship that we destroyed above this planet was not the only one in existence, and the Replicators currently in this city comprise of only a fraction of their entire population. There are many more out there, and they will continue attacking our kind until the attack command code is removed from their base code."

"Well, you should know that that was kind of the point," John retorted. "We're glad that they're kicking your asses."

"Whether or not you agree to help, we will not leave this city intact," the Wraith repeated, its voice unyielding. "The difference is, however, that we may allow you and your people to leave with your lives."

"Might. Might allow us."

"It is your choice. However, you have no chance of leaving this planet if you do not help us." As those words came out of the Wraith's mouth, John heard the sound of marching footsteps coming from the hallway outside the door behind him, and his heart plummeted. But they didn't belong to whom he suspected, and he watched, his expression surprised, as a group of Replicators entered the room and began attacking the four Wraith. With the Wraith suddenly distracted, he hurried to Rodney to untie him.

"You know, I seriously thought that I was going to become their next meal," Rodney gasped as John removed the gag from his mouth.

"Relax, Rodney," John replied. "Apparently, they like you more than me. Now let's get out of here." He motioned to the rest of his teammates and hurried out of the room, leaving the Wraith and the Replicators fighting behind them.

The ground suddenly shook as the team ran down the hallway, and John stumbled as the surface beneath his feet became unsteady.

"Oh, no," Rodney breathed, his voice carrying the apprehension that it always did when something bad was about to happen. "This city's about to blow."

Before John could reply, he heard Elizabeth inhale sharply, and he turned to see the corridor behind them come crashing down, the infrastructure collapsing and smashing into the ground and sending a massive blast of energy through the ground in his direction.

"Run!" John shouted. "Get back to the Jumper!" He was racing against time, leading his teammates through the endless corridors as the city shook more violently with every step taken. At one point, he was nearly knocked off his feet as the ground lurched suddenly, and he coughed as plumes of dust arose from massive amounts of debris, clouding the air and obscuring his vision as he struggled to see through the destruction.

As he rounded a corner, he stopped abruptly when he saw a group of Replicators marching toward him. He turned around, and he widened his eyes as the same appeared behind him and his team. The air around him suddenly felt colder, and he raised his ARG, firing at the Replicators, hearing his teammates do the same around him. But the Replicators continued approaching them from both directions, and eventually they stopped crumbling to the ground. The face of the black-haired Replicator was among those in the sea of endless replicating robots.

One Replicator punched him in the face, and the ground seemed unstable as he felt his arms pinned behind his back and himself being forced to his knees. He looked around him, realizing that three of his teammates were in the exact same position, and they were all surrounded by dozens of Replicators.

"Shall we do this here or take them to the brig?" one Replicator asked.

"There is no point in detaining them there when they will not leave this city anyway," the black-haired Replicator replied, his voice void of emotion. "Do it now."

John expected one of the Replicators surrounding them to approach him as they approached the rest of his team. Then he noticed that Elizabeth was not detained, and she was walking toward him, her eyes cold and narrowing. In a flash of movement, she raised his arm, and he felt an excruciating pain as his vision flashed white.


	4. Chapter 4

**Chapter 4**

John opened his eyes, and he was sitting in Elizabeth's office in Atlantis. On her table sat sculptures from different cultures on Earth, the Athosian pot that he had given her several years earlier, and a framed photo of her dog. Behind him, he heard numerous technicians and scientists running their business like it was a normal, uneventful day in the city. In front of him, sitting in her chair and wearing a red t-shirt, was Elizabeth Weir.

"Not much has changed, has it?" Elizabeth asked, her voice relaxed.

"I wouldn't really say that," John replied, keeping his tone light. "If you ask me, I think Rodney's kept his ego on a leash recently." Elizabeth chuckled softly, then leaned back in her chair.

"And Colonel Carter?" she asked. "How is everyone getting along with her?"

"People like her," John responded. "Mostly. Ronon's still kinda on edge around her. But she's doing a good job."

"That's good," Elizabeth said, smiling softly. "Though I can't say that I agree with the IOA's decision to place Atlantis under a military commander. But then again, I suppose I should have known that it was coming." John avoided her gaze.

"Do you remember the day that you found out about all this?" Elizabeth asked. "About Atlantis? The Ancients? The SGC?" John suddenly wasn't in Elizabeth's office anymore, and he was sitting in a control chair, though this one appeared different from that in Atlantis, and the cold temperature of the room signaled to him that he was in McMurdo.

"Yeah, I remember," he replied. "Carson fired a drone and nearly killed me and O'Neill." Elizabeth was standing beside him, shaking her head ruefully.

"Carson was very much a cowardly lion in the beginning," she said, her expression contrite. "But he, like many others in the expedition, soon realized what he was really capable of."

"Things haven't been the same without him," John said, his words barely audible.

"No, I bet they haven't," Elizabeth replied, her voice quiet.

The scene changed again, and John was standing outside on the control room balcony. The sky was dark with foreboding storm clouds, and the waves were coming in as heavy rain pounded down on the city's shield. Lightening electrified the stormy sky, and thunder reverberated through the air.

"You saved my life that day." Elizabeth approached him and leaned against the railing. "And the city. I think it was that day that I realized whom I could count on to protect the city and its people, no matter what." John looked at her, unable to say anything.

"And later, you asked for vacation twenty years in advance." Elizabeth tapped the railing and walked away. "I wasn't surprised that you somehow managed to keep your sense of humor in even the most trying circumstances."

Then John was in a lab, and in the middle of the room were two life pods. They were both empty, though it seemed as if the ghosts of those who had been stored in them were still drifting around the room.

"What happened that day was a result of poor judgment on my part," Elizabeth said, shaking her head. "I think I allowed the idea of enduring love to overwhelm me in that moment."

"Well, who doesn't love the idea of love, especially in this galaxy?" John said, half speaking to himself. Elizabeth turned to him, her eyes questioning.

"John, where do you find love in this galaxy? In Atlantis?" she asked. John was silent for a long moment.

"I don't know. But you don't know it's there until… it is." His words were barely above a whisper. He turned around and found himself in the infirmary, where a clear isolation tent was set up. Nearby was a powered off scanner, and in a corner lay several discarded red hazmat suits.

"You can be reckless at times, John," Elizabeth said, turning to him. Her gaze was serious. "But I know that you never do anything without believing that it's worth the risk." She placed her hand on his arm. "I can't say that I regret you doing what you did that time."

Then the shadows lengthened, and John was standing in an abandoned hallway. The lights shone eerily, and a cold chill ran through his veins as he realized he wasn't in Atlantis.

"They captured me, John," Elizabeth said, standing next to him. "And I was prepared to accept my fate. You and your team escaped, and you saved the lives of everyone in Atlantis and instigated conflict between two of the most formidable enemies in this galaxy." She looked into his eyes, her gaze unwavering. "If there was a price to be paid, then I am glad that we paid it." John swallowed hard, unable to meet her gaze.

"Well, I'm not," he whispered.

"I know," Elizabeth said, her voice soft. "But the situation couldn't have turned out any other way." She squinted hard at him. "And you need to accept that."

His heart felt like it was being raked across hot coals. When he looked up again, Elizabeth was gone. He turned around, finding himself alone in the ominous hallways, in the company of only the ghosts of his past, haunted by whispers of a time already long gone.

* * *

There was a piercing ache in his head as John regained consciousness. He twitched his fingers and stirred slightly, and as he slowly opened his eyes, he noticed the dim blue lights in the cold room as slats of metal material reached up to the high ceiling in all four directions.

"Sheppard." He heard Rodney's alarmed voice, and he shifted his head slightly and saw his teammates.

"Are you all right?" Teyla asked, her expression concerned.

"Second time today that my head feels like it's been split in two." John slowly rose to a sitting position, his head still in a piercing pain, and he leaned against the wall. "Looks like the Replicators changed their mind and still threw us in the brig." He then looked around him, realizing that their weapons were missing. Then someone else.

"Where's Elizabeth?" he asked. There was a moment of uneasy silence as his teammates exchanged a few apprehensive glances with each other.

"We do not know," Teyla replied, her face downcast. "We assumed that the Replicators took her."

"Though they obviously didn't play any mind games with her," Rodney muttered, massaging his head. "I mean, she hasn't left this planet at all, so there's no point –"

"She probed my mind," John interrupted, his voice barely audible. He watched alarmed expressions appear on his teammates' faces, laced with apprehension and worry.

"John, if Elizabeth has been compromised to such an extent…" Teyla began. And John felt his heart rushing again with emotions that he couldn't deal with, that he didn't want to deal with. If only to survive, he couldn't face them.

 _The hallways were dark and dimly lit aboard the Wraith ship, and John fired his weapon at a Wraith. As he prepared to turn a corner, he stopped upon realizing that Ford wasn't following him. He turned around, not believing his ears when Ford insisted to him that he go on ahead._

 _"John. I'll catch up. Now go!" And the last that he saw of Ford was the Lieutenant bolting off alone, disappearing into the maze of the unforgiving Wraith ship. As the alarm blared overhead and John darted off to find Teyla and Ronon, the image of his Lieutenant burned in his mind. One year ago, the twenty-five-year-old Lieutenant had been cracking jokes and grinning, always dependable in combat, always loyal to his people. And now… one eye was filled with a complete blackness, and his expression was always agitated and unsettled, as if something sinister had swallowed him whole. He had been a normal boy whose life and future had been stolen from him because a drug had twisted his mind, and he couldn't escape its clutches. Hell, he was just a boy. For a while, John had held on to some semblance of hope, even when it was clear that the Lieutenant was no longer thinking straight, that he could bring his fellow soldier and friend back. But the past couldn't be undone, and painful emotions threatened to burst out of his heart as he realized that the Ford that he once knew would never come back._

"Why are we still here?" Ronon grunted. John looked at Ronon, who shrugged. "We should be dead. Why hasn't this place been blown up?"

There was an abrupt noise behind John. He turned to see the door open, and three Replicators, including the one with black hair, entered the ominously lighted room. The Replicators marched in synchrony as they approached, their movements sounding rehearsed, their eyes filled with darkness.

"The Wraith ship above the planet has been neutralized," the black-haired Replicator spoke, its tone emotionless. "And we have returned in greater numbers to assume back control of our city."

"Where's Elizabeth?" John demanded, stepping in close to the wall so he could see the full faces of the Replicators in between the metal slats.

"Dr. Weir has been taken to be returned to stasis," the Replicator responded. "For the moment, she has served her purpose."

"If you wanted her to probe my mind," John began, his voice low and menacing, "why didn't you do it earlier? Why delay the act?"

"It was necessary to wait until more of our kind returned from afar to defend our city," the Replicator replied. "Based on information already stored in our archives, we knew that Dr. Weir would not leave this city because she viewed herself as a threat, and you would not leave her behind if she did not appear to be of immediate danger to you and your people."

"It was a trap," John heard Rodney say aloud, his voice agitated. "They waited until they returned before they made her turn rogue on us."

"We found it impractical to act earlier and sacrifice a number of our kind before we could successfully detain you and your people. On the contrary, we knew that you would never harm her."

"Why didn't you just stick your hand into my head yourself?" John demanded, feeling his blood cold as he realized the truth behind the Replicator's statement. "Why did you have to go through her?" The Replicator appeared to tilt his head slightly.

"There is one matter that surprises even us, Colonel Sheppard," the Replicator replied in a toneless voice. "We did not command her to extract information from you. Dr. Weir acted with full autonomy." John felt as if his entire body was paralyzed.

"No."

"She was able to successfully obtain information regarding Atlantis' current location from you, Colonel Sheppard, and transfer it to the entire collective," the Replicator continued. "Thanks to newly gathered information from Dr. McKay as well, we are already in the process of figuring out how to remove the Wraith attack directive from our base code." The Replicator's voice was void of emotion. "Within the hour, our base code will be amended, and we will send our forces on course to Atlantis to destroy it."

"We're gonna get out of here," John said, his voice rising. "We're gonna get Elizabeth, and we're gonna get back to Atlantis and warn our people."

"Your words carry lost hope," the Replicator responded, his voice toneless.

"Maybe they do, but who would I be if I didn't try?" John retorted.

"The Dr. Weir whom you knew no longer exists." The Replicator's gaze bored into John's eyes. "Perhaps you simply need some convincing."

There was an ominous click that echoed in the room as the door opened again. A group of four Replicators marched in, two by two. In their middle was Elizabeth, her head held high, her face completely expressionless.

"I thought you said she was being taken for stasis –" Rodney began.

"There has been a slight change of plans," the black-haired Replicator replied, its tone emotionless.

There was a portentous hum as the force field to the brig was turned off and the door slid open. The Replicators stood aside, and without hesitation, Elizabeth entered the brig and approached John. She raised his arm, and John felt a powerful pain in his gut as she threw him a violent punch. Doubled over and barely able to breathe, he looked up to see Elizabeth standing above him, her eyes hardened, her face completely inexpressive. She hit him again, this time in the face, and he fell over. His vision was fading to black, and he couldn't make any words come out of his mouth, barely able to endure the storm that was raging uncontrollably in his heart.

* * *

"John? John, are you all right?" John was sprawled on the ground, and he heard a voice. He slowly rolled onto his back, groaning softly at an ache in his abdomen and the left side of his jaw. He opened his eyes, and he saw Elizabeth's concerned face.

"I'm very sorry. I had to make it look convincing," Elizabeth said, her tone apologetic. John looked around him, and he saw his teammates standing behind her, looking just as bewildered as he felt.

"Elizabeth? What just happened?" he asked.

"Elizabeth attacked you, and you passed out again," Rodney's voice came from a few feet away, though his griping tone still sounded uneasy.

"That's the third time today," John muttered. His mind still felt unclear, but he noticed that the door to the brig was open, and there were no Replicators in the room. He looked back at Elizabeth. "What happened to you, and where are the rest of them?"

Elizabeth sighed. "I had to make a very convincing argument to them to leave me alone with you and your team." She looked around at John and his teammates. "Look, we don't have much time," she said. "I transferred to the Replicators the gate address to an uninhabited planet – they don't know where Atlantis really is." John squinted at her.

"Are you saying –"

"That I was never taken control of by the Replicators? Yes." Elizabeth looked repentant. "Probing your mind – not exactly the most pleasant task that I've been forced to carry out with you, but I couldn't risk them gathering accurate information about Atlantis." There was a surprised exclaim from behind her, and John looked over her shoulder to see Rodney's stricken face.

"Wh – I can't believe –" Rodney stammered. "– You hoodwinked them!"

"And us," Ronon grunted. John looked back at Elizabeth.

"They don't know?" he rasped.

"No. Not yet at least," Elizabeth responded, her voice firm. "They haven't discovered the false gate address yet, but they will once they get there." She paused for a moment. "Unfortunately, I wasn't able to tap into the system to alter Rodney's information about the Wraith attack command code, so they are working on making changes to their base code to shut off the command right now."

"Well, we can't do anything about that right now," John said. "We need to get out of here."

"I need to stop them." Shocked, John looked at Elizabeth's determined face, as if he couldn't believe her words. "John, if the Replicators successfully shut off that attack command, they and the Wraith will no longer be in conflict with each other –"

"No!" John cut Elizabeth off. He sat up suddenly to meet Elizabeth's level gaze beside him. "I'm not about to let Rodney loose in the city to work on that anymore, and you're not going to, either. We need to get out of here, and I'm not about to do anything that means giving up one of my own people – again."

"John, you can't stop me," Elizabeth insisted.

"Don't argue with me!" John shouted, standing up, and Elizabeth rose to her feet with him. "You're coming with us, even if we have to stun you and carry you back to the Jumper. We're leaving right now."

Then no one spoke, and an uneasy silence filled the air. John looked straight into Elizabeth's adamant eyes and saw that her expression had hardened with stubbornness. He felt a sense of fury nearly boiling over within him.

"Sheppard, how do we know she hasn't been playing us the whole time?" Ronon's voice broke the strained silence. John continued to look at Elizabeth, though he felt something in his heart beginning to fade.

"John, Ronon is correct." It was Teyla speaking now, and her voice was soft. "As much as we would like to trust Elizabeth, we have reason to be skeptical now."

"You have every reason not to trust me," Elizabeth spoke aloud, still staring at John. "In a way, I'm almost relieved to finally hear that."

There was the sound of a distant explosion, and the ground trembled slightly. John looked up, hearing faint sounds of something crashing down above them.

"What was that?" Teyla breathed.

"I don't know," John replied, "but the Wraith did say that they had detonators planted in the city. Must have been their back-up plan to blow this place up if they had to do it remotely." He looked at his teammates. "We need to go," he said, and they nodded and hurried out of the brig and into the hallway. Elizabeth was still standing next to him, and he looked at her, whose expression remained hardened. Wordlessly, she turned away from him and ran out the door, and he followed her.

He led his team through the dim hallways that were growing more unsteady with every passing second. There were no Replicators around now, and they climbed a stairwell, then turned a corner and spotted the ladder to the hatch from which they had entered. Guarding their six, John motioned for Teyla ascend first, followed by Rodney and Ronon. He signaled to Elizabeth to go, and she turned around, her expression obstinate.

"Elizabeth?" He looked at her, his eyes fearful of what she was about to say.

"John, if the Wraith are about to destroy this city, then it's best that I remain behind."

"No, it's not. You're coming with us!"

"No, I won't!" Elizabeth shouted. John was startled by her outburst, and his face slightly fell. He watched as she narrowed her eyes before she spoke again.

"It's better for the both of us."

John felt something inside of him snap.

"Then you leave me with no choice." In a single motion, John pulled out his 9 mil and pointed it at Elizabeth's leg. A shot rang through the air, and Elizabeth gasped, her eyes widening, suddenly lurching to one side as she lost her balance. John caught her before she fell, then hoisted her over his shoulder as he climbed the ladder himself.

"Sheppard, we thought you'd been killed!" Rodney exclaimed as John emerged with Elizabeth. John felt Elizabeth struggling against his arms, her breathing sounding panicked, and he saw Rodney's eyes widen. "Wh –"

"Elizabeth was about to run off, and I wasn't gonna let her." John suddenly felt a powerful pain as Elizabeth punched him hard again in the side, and he was forced to set Elizabeth down on the ground, then staggered forward, breathing heavily, fury nearly bursting out of him, out of control.

"Will you just –"

"John, I won't go," Elizabeth interrupted. John watched in startled amazement as she rose to her feet, the flesh wound in her leg apparently healed. "As long as my nanites are active, they make me dangerous, and you need to accept that there is absolutely nothing you can do to change that."

"Look, when we get back, we'll put you in isolation, and Rodney will figure out how to repair your cells and shut down the nanites –"

"No, John," Elizabeth cut him off, her tone uncompromising. "Even if they are shut down, you can't ensure that they will never be reactivated again and used against us." John felt the rooftop they were standing on begin to tremble, and he took a step toward her, clenching and unclenching his fists.

"Look – you're a member of my team, and at the end of the day, no matter what happens to any of us, we don't give up on each other."

"John, this mission was a mistake." Elizabeth's tone was accusatory. "You've endangered the entire Atlantis base as well as the lives of you and your team, and you appear to have not even considered the possibility that being rescued was not at all what I wanted." Her expression appeared injured. "The least you can do now is to allow me the dignity to choose my own fate."

"You want to throw your life away, just like that?" John retorted, taking another step toward her. "I'm not buying it, not while there's still a chance that we can save you." His eyes bored into Elizabeth's. "You didn't deserve this, and what happened to you wasn't your choice!"

"You're right." Elizabeth held John's gaze, her eyes resolute. "It wasn't my choice. Had I had any say in the matter, I would have died rather than allow something immeasurably dangerous to keep me alive. But that clearly wasn't my decision to make." She stepped closer to him, and he could feel a mixture of negative emotions washing off of her. "But I had the choice of going on the mission to this planet to save our city, and I did what was necessary to allow you and your team to escape – even if that meant not coming back."

The sound of explosions began going off all over the city, and John distantly heard the voices of his other teammates, pleading to him that they needed to leave. It felt as though he had already lost, and he was only clinging on to the last shred of hope before the inevitable happened. As the ground beneath him became increasingly unstable, he suddenly felt the intense frustration and anger, everything that had been building up all this time, a whirlwind of painful emotions that he had tried so hard to suppress.

"Elizabeth, I went through this with Ford." John seized Elizabeth's arms as if his life depended on it. "I assumed every possible risk in this damned galaxy in order to come back for you. Why? Because we don't leave our people behind, no matter what happens to them, no matter the cost." His eyes became desperate. "I already left you once. Don't make me go through that again." Elizabeth looked at him, and he saw that her expression had changed, her adamant resolve having faded away to something akin to remorse.

"John, you knew when my nanites were reactivated that there would be consequences. They're here now – and we have to accept them." John felt something inside him wither.

"Elizabeth –"

"I'm sorry, John. You can't save me." Elizabeth looked at him once more, her expression pained. "You read my letter. Even if I go back, there's no going back to the way it was before all this happened, and you need to accept that." She broke free of his grip and whirled away from him, her hair flying around her, and John watched in horror as she disappeared down the metal hatch.

"Elizabeth!" His shout was drowned out by the sounds of roaring explosions, and he felt arms grasping onto him. He resisted, struggled against their grip as they pulled him away, almost unaware of the fractures forming in the surface beneath his feet. Then there was a deafening detonation, and John felt himself flying through the air, smashing his head against what he assumed was the hull of their Puddle Jumper. His eyelids dropped, and the last thing he saw was the panicked faces of his teammates, minus Elizabeth, before his vision went completely black.

* * *

His mind and body felt completely numb. He twitched his fingers, and he sensed bright lights through his closed eyelids. He shifted slightly, and there was a dull aching in his entire head.

"John?" He faintly heard a voice. John raised his eyelids halfway, trying to keep out the light, and he glimpsed Teyla's face, looking concerned.

"John, can you hear me?" Teyla's gentle voice drifted to his ears. His gaze slowly focused on her, looking confused.

"Where am I?" he rasped. Teyla seemed to hesitate for a moment before responding.

"John, you are in the infirmary. You have been here for nearly a day." Her expression seemed disquieted.

"What about Elizabeth?" John asked. He watched as Teyla's eyes widened, as if she was startled, and her expression suddenly turned sober.

"John, you fell unconscious in the Jumper when we were caught in the crossfire between the Wraith and the Replicators. You suffered a severe concussion, and the Jumper was severely damaged." Her voice was soft. "Major Lorne and a team of Marines were in another Jumper when they found us in space, and they escorted us back to the Gate and back to Atlantis." Teyla's gaze was somber.

"John, the mission did not succeed. We never made it to the planet."


	5. Chapter 5

**Chapter 5**

The door to Colonel Carter's office closed softly behind him, and John watched as Colonel Carter went around her desk and took a seat before him. Her blond hair was gathered at the base of her head in a loose bun, and a composed expression graced her face.

"How are you feeling, Colonel?" Carter asked, her voice soft.

"Been better." John avoided her eyes.

"We were lucky that Major Lorne's team found you and your team when they did. A little while longer, and your Jumper would have begun losing life support, and your injuries might have become even more exacerbated." John didn't say anything, and Carter seemed to hesitate before realizing that she needed to speak first.

"Colonel, you realize that I could dismiss you from your post here in Atlantis after this, right?" Her words were soft, and there was nothing in Carter's voice that indicated recrimination.

"Yeah."

"What were you thinking? Disobeying direct orders, no plan at all. I told you two weeks ago that I would have approved of a rescue mission if you could present me with a viable plan." Her voice was unwavering, but she looked as if she were honestly trying to understand something. "I'm not unreasonable, Colonel, and I would have let you go after her if you were able to convince me with a workable plan."

"Rodney was taking too long, and I couldn't wait any longer."

Carter looked down at her hands, looking as if she were trying to figure out what to say. "Colonel – I hate to say it, but you could have asked me for help." She paused for a moment, as if she were forming her thoughts carefully. "I realize that perhaps this should have been higher on my list of priorities when I got here a few weeks ago, and I'm sorry that I didn't offer my assistance at the forefront. I know that you were holding discussions with the IOA over video transmissions before I arrived, and I permitted you to return to Earth to talk with them in person. And I'm sorry that the discussions didn't go as well as you might have hoped." She leaned forward slightly. "But Colonel, you didn't have to do this alone. We could have worked together with McKay to come up with a doable plan. It's not like the thought of leaving Dr. Weir behind with those Replicators sits well with me, especially when she's the reason that all of you are here right now."

"Maybe I just have some trust issues. I don't know who I can count on anymore."

Carter looked down again, her expression contrite. "Look, Colonel – I'm very sorry about what happened to Dr. Weir. I've been involved in the SGC for ten years, and I've had my fair share of experiences where I've lost people. And it hurts. I suspect that you and Dr. Weir must have been close – it's hard not to be when you're facing life and death together. And I can't imagine what you must be going through right now." She tapped her fingertips on the table, blinking rapidly a few times before speaking again. "However, as much as I want to approve of a rescue mission for her, after what happened four days ago, I can't do that. And I'm very sorry." John didn't respond, and Carter paused for a moment, as if she were making a final choice for what she was about to say.

"Colonel, I'm not going to write you up."

Upon hearing those words, John looked up for the first time since he sat down in Carter's office, a stricken expression appearing on his face. Carter's tone was placid, and she looked at him with an unperturbed gaze.

"There's no doubt that I should, but if I turn in a report on this, the SGC will remove you from your post in Atlantis and demote you, and I can't imagine you getting away from this without a court martial." She paused for a moment, and a hint of skepticism flashed briefly over her face before resolve turned. "What you did was obviously reckless and unacceptable. But while it's my responsibility to ensure that those under my command follow my orders and to ensure the safety of this base, I'm aware that Dr. Weir chose you for this expedition for a very specific reason, not only because you had the Ancient gene, but also because she saw something in your record that she considered an asset. The fact that she insisted that you be promoted two years ago and remain ranking military officer at the time, I think, says a lot about how much she trusted your judgment and leadership, and at the time, she also had the support of General O'Neill. This mission is a dangerous one, and considering that you and your people are still here after three years in this galaxy, you've clearly done a good job overall." She paused for a moment, as if allowing her words to sink in. "While my way of doing things may be different from Dr. Weir's, I can understand why she felt that you were valuable to this expedition. So I'm willing to allow you to stay and make this new power dynamic work out between us." Carter looked down again, pausing for a moment before continuing.

"Also, I don't think the expedition members can handle another change in leadership right now." Her voice was quieter now. "I understand that Dr. Carson Beckett was killed a few months ago, and seeing as how you've earned a lot of respect here, I think it'd be too much of a shock for the expedition to lose another one of their senior staff right now." She looked up at John, her expression open and honest. "The only people other than me and your team who know about this are Major Lorne and his group of three Marines who went to rescue you, and I've asked everyone to sign a contract that binds them to confidentiality."

Upon hearing all this, John found himself completely at a loss for words.

"Thank you," he said, his voice not feeling whole.

"You're welcome," Carter replied, her voice soft. She looked down again, as if hesitating with her next words. "Dr. Heightmeyer knows as well." John looked up at her, feeling a sense of consternation wash over him.

"I'd like for you to talk to her, Colonel." Carter's expression was filled with sympathy. "You're not returning to your daily duties until you meet with her and she tells me you're ok."

* * *

 _Twenty-eight hours later_

Dim lights shone overhead in the empty mess hall that night, and John sat alone in the middle of the room. He raised a cup of cold coffee to his lips, grimacing at the taste, and he set it back down. He heard footsteps approaching from behind him, and he watched as Teyla came around to the opposite side of the table.

"Mind if I join you?" Teyla asked.

"No, not at all," John replied. Teyla took a seat across from him, folding her hands together.

"Dr. Heightmeyer asked me to talk with you," she said.

"I know. She figured that you might have better luck with me than she did," John replied, and he saw the corners of Teyla's lips curve upward slightly.

"How are you feeling?" Teyla asked.

"Now, you see, that's the question that I have trouble answering," John responded, sitting back in his seat. Teyla looked down at her hands, as if trying to figure out what to say.

"John, when you read Elizabeth's letter…" She stopped, as if prompting John to speak. For a moment, John remained silent.

"Did you know that she was going to step down?" He avoided Teyla's eyes.

"She confided in me about the possibility." Teyla's voice was quiet. "She was quite upset that the IOA and Earth's military intervened in Atlantis' affairs without consulting her first, and it would appear that she believed that her services were no longer respected, and she had no choice but to step down. I suspect that she wrote her resignation letter when we were still trying to elude the Replicator beam back on Lantea." Teyla took a deep breath. "Even though she had imparted to me this possible decision, I did not believe that she would arrive at this resolution so quickly, even before we had left the planet."

"It's just like her," John said, half speaking to himself. "She locked herself into a decision, and she would have left the moment she could. No hard feelings." He tapped his fingers on the table, and he suddenly felt exhausted.

"I feel like karma has come to bite us all in the ass. None of this would have happened if…"

Teyla seemed to grasp for appropriate words. "It is useless to agonize yourself over what-ifs. However difficult it may be, we must learn to accept what has happened." John didn't respond, and Teyla was quiet for a moment before speaking again.

"John, I can understand the incredible distress that one experiences mentally as a result of not knowing the fate of someone close to you." She stopped for a moment, blinking rapidly before taking a deep breath and continuing. "I understand that you are a man of action, and I realize that being unable to go back for Elizabeth must create a sense of helplessness." There was a moment of long silence, and John slightly lifted his hand off the table, as if grasping for words to express what could not be expressed.

"I should be dead. I've cheated death more times than I care to count in this galaxy." He struggled to suppress the emotion building in his throat. "How is it that I'm still here, but…" John trailed off, unable to speak any further.

"You cannot blame yourself for what happened to her," Teyla said, her voice quiet, and she took another deep breath. "In a way, Elizabeth chose her own fate, and we must respect her decision." John didn't speak, and he looked down.

"In her letter, Elizabeth requested that you remain ranking military officer in Atlantis." Teyla spoke again, her voice hesitant.

"Yeah, well, that didn't really happen," John mumbled. Teyla seemed to hesitate before continuing to speak.

"I remember the first few months here in Atlantis, when it seemed that you were still trying to become accustomed to your new position among the military contingent here. And in the past few years, I have seen you gain a tremendous amount of respect among soldiers and civilians alike." She looked down at her hands, as if trying to figure out what to say next. "I realize that Elizabeth trusted you without reservation, for both work and personal reasons. And I sense that you feel as though you must repay the debt in some way." John didn't say anything for a long moment, and it felt as if a hidden truth had just been exposed.

"Three years ago, I was just a damn Major who didn't know what the hell he was doing with his life." His voice carried a sense of despondence. "Then all this craziness happened because she wanted me here. I told her she was making a mistake… but she insisted."

"Why did you doubt Elizabeth then?" Teyla asked, her voice quiet. There was a long silence, and John struggled to respond.

"Thought I'd just screw everything up." His voice was barely audible, and Teyla looked as if she were placing considerable thought into her next words.

"John, if you were not here, many more people may have died in these past few years, and Atlantis may not still be here. Your bravery and courage are admired by many people in Atlantis, and you have allowed many despairing worlds in this galaxy to believe in a better future. And what is more, you have allowed Ronon, Rodney, and myself to feel that we have someone whom we can trust with our lives." John didn't respond, and Teyla was quiet for a moment before she spoke again.

"Last year, when Ronon was captured by the Wraith and we went to rescue him on Sateda… I remember thanking you for going after him that way. And I feel that I should thank you now for trying to go back for Elizabeth, despite what has happened." John vaguely saw Teyla's hands reach out to his. "You are a good man, and your loyalty and courage are among the most steadfast of those of anyone whom I have ever known. And I believe that Elizabeth felt the same way." John struggled to speak.

"I feel like… I _owe_ her. For everything." He felt Teyla squeeze his hands tightly.

"Had your positions been reversed on the Replicator planet, you would have done what she did." Teyla's voice was soft. "And she would be mourning your loss right now."

* * *

 _Ten hours later_

John walked over the bridge, spotting Rodney among the computer consoles in the control room. Only two other technicians were in the room, and the Gate stood majestically below them. The early morning light filtered in through the stained glass windows, casting soft shadows in the Gate Room.

"How's it going, Rodney?" John asked as he approached.

"Well, the mess hall's almost out of coffee, and Zelenka's been delinquent in his reports for that new lab we found near the east pier," Rodney muttered, squinting as he held up an unfamiliar piece of Ancient technology. "But other than that, just fine."

"Just wanted to let you know that I'm going out to the mainland," John said. "Carter's cleared for me the use of a Jumper."

"Yeah, sounds – wait, really, Sam's letting you?" Rodney asked, suddenly looking up from his work.

"Yeah, though she said I had to take someone with me," John replied. "So Ronon's coming along."

"Oh." Rodney looked surprised. "Well, all right then." He turned back to his work, and John began heading out of the control room. Then he stopped, and he turned back around.

"Rodney," he said. Rodney looked up again.

"Yeah?" Rodney asked. John took a step closer, struggling to get his words out.

"Thank you for trying. I know you… did your best."

Rodney's surprised face turned somber, and he appeared to be at a loss for words.

"Sheppard, I…" Rodney trailed off, apparently having as much trouble as John was at expressing himself. He looked up, his eyes full of remorse. "You're welcome."

John looked at Rodney's regretful expression, and he nodded and turned away.

"Sheppard." He turned around again, and Rodney seemed to hesitate for a moment before stepping toward him and pulling him into a fierce embrace. Startled, John felt his arms raise slowly before he awkwardly patted Rodney on the back. A few seconds elapsed before they broke apart, and Rodney's face appeared a bit red.

"I miss her, too," Rodney mumbled, then turned away and stumbled back to his computer. Before John could react, he heard heavy footsteps behind him.

"Sheppard, you ready?" Ronon's voice sounded in the control room.

"Yeah," John said after a moment longer than necessary. "Let's go."

They headed up the stairs leading to the Jumper Bay, bumping into a group of Marines along the way, and John saw that Major Lorne was leading them.

"Sir." Lorne nodded his head in acknowledgement of John's presence.

"Lorne. Good morning." John watched Lorne and the Marines step aside, allowing him and Ronon to pass. As he headed into the Jumper Bay and entered a Jumper, John couldn't help but feel that he had detected a hint of apology in Lorne's eyes.

When the Bay doors opened, the Jumper rose and flew up into the blue skies over the vast, glittering ocean. John looked up at the HUD and saw that the weather appeared clear around the mainland area. There would be no storms that day.

He landed the Jumper in an open area on the mainland, their nearby surroundings filled with plenty of shrubbery, and large trees reached up high above him, the morning sun casting cool shadows on the ground. John headed into the forest, hearing Ronon's large form lumbering along behind him. Twigs snapped beneath his feet, and he hoped that his and Ronon's disturbance would scare off any poisonous snake-like creatures lurking around them.

John stopped at the base of a large tree, and he settled down on the ground, placing his weapon beside him. He leaned back against the trunk, stretching his legs out in front of him, and he folded his hands together on his lap. He heard Ronon settle down next to him, facing his left, and for a while, John allowed his gaze to meander aimlessly, seeing only green trees above him, bathed in warm sunlight, and cool shadows danced across the ground.

He didn't know when he closed his eyes, but he was awakened upon feeling someone shaking his shoulder.

"Sheppard." Ronon was next to him. "It's been an hour. We need to get back." Reluctantly, John allowed Ronon to help pull himself up, and they trudged back to the Jumper.

They were soon in the skies again, over the blue waters as they flew back to Atlantis. There seemed to be a sense of serenity in the air that day, with the sun shining down on the ocean.

"You know, it was nice of Carter to let you stay." Ronon's voice broke the silence.

"Trust me, I'm just as surprised as you are," John replied.

"Wouldn't have happened to any of my men on Sateda." John glanced at Ronon, unsure of whether to feel sorry or suspicious at Ronon's words.

"For the record, you didn't do anything wrong." Ronon continued speaking. "When Melena refused to leave, I stayed with her until the very end." John turned toward Ronon, shocked at Ronon's words.

"What are you say –"

"I'm not implying that there was anything going on between you and Weir," Ronon cut him off. "Hell, after what you've been through this week, I sure hope not. What I mean is, you two obviously depended on each other for a lot of stuff. And how could you not in this galaxy?" He leaned back in his chair. "We all need someone to have our backs when no one else has them. Melena was that person for me. And while you've got your team, I know that Weir supported you in ways that meant a lot to you." He looked at John, who was watching him with a shocked expression as he spoke. "Was anything that I said just now wrong?" John turned away, unable to make any words come out of his mouth.

"I'm not answering that question," he said after much longer than necessary.

"I'll take that as a 'no,'" Ronon replied.

"You do realize that I brought you along this morning because I knew you wouldn't talk?" John retorted as Atlantis came into view.

"Well, you thought wrong." Ronon leaned forward. "I might not talk much, but I talk when I have something important to say."

John turned away, and he didn't say anything for the rest of the flight. After he flew through the Jumper Bay doors and landed, Ronon walked out the Jumper without a word, leaving John alone inside. A long moment passed before he got up and headed out the door, his footsteps echoing in the empty room.

He found his teammates in the mess hall, gathered together at a table and talking over breakfast. John went to get his food, then joined his team, settling down next to Rodney with Ronon and Teyla across from him. As he poked at his food, his eyes rested on two empty chairs at the table, and he felt a pain strike his heart upon thinking about who could be sitting with them that morning. Then he realized that his teammates' conversation stopped, and they all had subdued expressions on their faces.

"What?" John demanded. "Keep talking."

"Oh – well, it's – it's nothing," Rodney stammered, sounding nervous. He turned away, as if avoiding conversation.

"McKay's just upset because there's only decaf left," Ronon said, smirking.

"No wonder I couldn't concentrate this morning. You can't run a city without power," Rodney grumbled.

"John, I was wondering if you would like to practice bantos fighting with me this afternoon," Teyla said, turning to him.

"Uh, sure, why not?" John replied.

"Good," Teyla said, smiling. "It has been a while since we have practiced, but I am assured that you will be fine." John looked around at his teammates. The pain in his heart was still there. Yet, upon seeing familiar faces in front of him, he felt a momentary sense of respite.

"Yeah. I'm sure I will be."

* * *

 _Nine days later_

The waves rolled in the distant darkness, and two moons shone overhead, slightly obscured by the clusters of misty clouds drifting in the black sky. The mess hall balcony was empty now – just as his teammates had trickled in one by one that night, they had also gradually disappeared as the night grew late, eventually leaving John alone once more. A half eaten bowl of nibbles and a magazine sat on the table before him, and he looked out into the calm night and heard the ocean in the air.

"It's beautiful, isn't it?"

John turned around and saw Elizabeth sitting across from him, wearing her Atlantis jacket, and her hair blew softly in the wind.

"You're not really here," he said.

"No, I'm not." Elizabeth continued to look out at the dark ocean waves. "But you apparently didn't want to be alone. So here I am." John looked at her before his own gaze returned to the ocean.

"We lost Heightmeyer today," he said, his voice low.

"I know," Elizabeth replied, looking down. "I'm sorry."

"I didn't know her that well. But she and Teyla were good friends." John looked down, and his voice was barely above a whisper. "It's my fault she's dead."

"You can't blame yourself for what happened." Elizabeth's voice was soft.

"I hardly think that stalking people in their dreams as a sadistic sociopath doesn't cross some sort of line," John replied. Elizabeth turned toward him.

"You saved Rodney. And yourself."

"More like kicked my own ass." John looked at Elizabeth. "Do you have any idea how unsettling it is to see a Freddy Krueger version of yourself?"

"No, but I have seen myself aged ten thousand years."

"That's a tough one to beat," John said, sighing.

"No, I'd say we're about even now." Elizabeth tilted her head, her face thoughtful. She then looked at him, and her expression became serious. "You're afraid of yourself, huh?" John didn't respond, and she sighed quietly. "For what it's worth, you're doing your best. That's all you can ask for from yourself."

"Apparently, it's not enough." John looked away, feeling something painful in his heart. "People keep dying," he whispered. "It's hard enough to accept when a mission goes wrong, but it feels a lot worse recently. We lost Carson, and I don't know where you are…" He trailed off, and Elizabeth looked out at the ocean, her expression pensive.

"It can't be helped," she said in a quiet voice. "And we don't have much choice but to move on from here. Otherwise, we risk allowing the ghosts of our past to haunt what we have now."

"But what's left?" John murmured. Elizabeth turned toward him.

"John, you still have your team." Her voice was soft. "And they care very much about you and your well-being. And there are many others in Atlantis who look to you. Do it for them."

"I…" John trailed off, suddenly realizing something that he didn't want to admit. "Ronon was right," he said aloud, and Elizabeth looked surprised.

"About what?" she asked. John avoided her gaze, and there was a long silence.

"Nothing." He turned away, trying to conceal his emotions. He was silently relieved when Elizabeth didn't press him any further.

"You're still out there," he said after a long moment. Elizabeth turned to him.

"You really believe that?" she asked.

"I'm not giving up, not while there's still a chance." John suddenly looked up at Elizabeth. " _Are_ you?" Elizabeth gave a small smile.

"Maybe," she replied. "I honestly don't know myself. It feels as if I'm in a deep sleep." She looked out toward the ocean. "You know that I would never want to return if it meant putting the lives of everyone in Atlantis in danger." Elizabeth turned back to John, and her expression was contrite. "But I know you, John. You've changed quite a bit over the past few years, but something I know will never change is your loyalty to your people. And I guess that includes me." She looked squarely at him. "Even if I told you a thousand times over not to come back for me… I know you won't give up until you find a way to get me back."

"There's still hope," John whispered. Elizabeth smiled softly.

"Perhaps there is. For the moment, at least."

John looked back out toward the ocean, listening to the distant waters, and the moonlight shone down from above. When he turned back around, Elizabeth was gone. He tapped his fingers on the tabletop, then grabbed the bowl and magazine and got up.

The hallways were empty as he headed back to his quarters. The dim lights seemed calmer now, less ominous than they had been as of late. As he swiped open his door and it swished shut behind him, John walked over to the window and looked out at the city. He gazed upward toward the night sky, as if searching for something in the moons above. Standing there, gazing out at the quiet night, he felt more alone than ever before.

John turned around and looked at his nightstand, and he picked up a worn sheet of paper that he had read countless times over. He rubbed his eyes wearily as he looked over Elizabeth's resignation letter again, and he could almost hear her voice that was filled with bitterness and regret, carefully shrouded under a tone that seemed to convey apology. But she had had nothing to apologize for.

The universe truly was out to bite all their asses.

John set the letter back down, and he sat down on his bed. His mind drifted, and he was trying to picture her face, remember her voice, cling on to a sense of normalcy that he had felt from all those times they had talked in her office or outside on the control room balcony. But that sense of normalcy was now shattered, and he was left broken and limping, trying to pick up the fragmented pieces, not lose himself over grief and anguish.

He was living in a present in which he almost didn't want to wake up the next morning, not knowing what would happen the next day. It was inevitable that he would lose someone else, and he didn't know how much more pain and grief he could endure. The universe had become too volatile for his tastes, and John felt as if he had already suffered enough for a lifetime.

 _He stormed into Elizabeth's office, his mind seething as he leaned against her table, not really caring, in fact, if he did end up causing political trouble from decking an IOA bureaucrat dressed up in a stuffy suit._

 _"I've never seen you like this. What did Woolsey say to you?" Elizabeth looked at him curiously._

 _"Besides judging every damned decision you've ever made?" John fumed. He watched as Elizabeth leaned back in her chair with an amused expression on her face._

 _"John Sheppard, are you defending my honor?" Her tone was playful, and caught off guard by her question and suddenly realizing how his words were coming across, John needed a moment longer than necessary before he could respond._

 _"And judging me for agreeing with you."_

He had never before felt so exhausted. Lying down, he closed his eyes. Ronon had been right. It would be easier if she were here.

He allowed himself to surrender to the unconsciousness. There, he detected the faintest hope, drifting aimlessly as if it were in a deep sleep, waiting to open its eyes. But until then, he was to pull through alone.

He would see her again. Even if it was only in his dreams. And he would find her and bring her back.

* * *

 _Author's notes - fairly extensive ones at that - are included in the next and final page._


	6. Author's Notes

_I totally didn't expect to write something this long for author's notes, but it happened. For those of you interested in my thoughts in the process of creating this story, here's a nice, long reflection._

* * *

 **What Dreams May Come: Author's Notes**

* * *

 ** _Writing fueled by emotion: Introduction_**

 _The act of writing has always served as a way for me to cope with my emotions. I journal on a regular basis – I remember the pages of my first entry, me writing the alphabet with a lime green crayon – and as someone who is deeply in touch with her personal emotions, I also find myself drawn to people in general and everything about them: behavior, actions, motives, thoughts, feelings, relationships, conflict, backstories. While the world of SGA and its characters are fictional, I have always been greatly captivated by its characters, and I enjoy using fanfiction to explore many aspects of their characterizations and to portray their complex emotions and their deepest humanity._

 _I have recently been re-watching SGA after being disconnected from the show and fandom for several years. The last time that I was involved in the show and fandom, I was greatly upset with many of the casting decisions made at the end of Season 3, one of them being reducing Torri Higginson to a recurring cast member, which, for all intents and purposes, took her off the show entirely. I think that I have been wanting to write this story for a long time now, and by that, I mean that I have been wanting to write a story that addresses the aftermath of Elizabeth's capture by the Replicators on the remaining main characters in order to help me better cope with her absence in Seasons 4 and 5, since writing has always been a kind of emotional therapy for me after all. Though I didn't quite know how I would approach this objective at first, the manner in which I would find a sense of emotional peace turned out to be writing this story with three primary goals: 1) write a story that respects canon events but is realistic to the extent that it could contribute to what happened on-screen; 2) rectify what I felt were two major flaws on-screen: an inconsistency between John Sheppard's quintessential belief in not leaving people behind and the absence of an on-screen rescue mission for Elizabeth, and what I felt was a disrespectful manner in which Colonel Carter was introduced to Atlantis, both to Colonel Carter's character and her predecessor's; and 3) further acknowledge John's emotions toward Elizabeth's loss, which I would have appreciated to see more fleshed out on-screen. Not only have I been extremely excited in having completed this piece of work and sharing it with others, but I'm also grateful that in writing this story and fulfilling the aforementioned goals, I've at long last been able to accept events as they occurred on-screen, obtain a sense of emotional peace, and appreciate Seasons 4 and 5 for what they are._

* * *

 ** _Respecting canon events: The rescue mission that never happened_**

 _I most enjoy writing fanfiction that I myself would have thought realistic enough that it could have actually happened on-screen. As such, in order to respect canon, I never once considered writing a story about a successful rescue mission for Elizabeth, because that would have meant entirely repudiating the last two seasons of SGA. I personally didn't want to complete this story in a state of denial about Elizabeth's fate – I'd been there too long already, and the purpose of this story was partially to help me accept what really happened. However controversial they were, I wanted to respect canon events as they were, and I wanted to write a story that honored the actual episodes while still being something that could have contributed to on-screen events._

 _I had arrived at the conclusion that John went on a failed, off-screen rescue mission for Elizabeth – more on how I arrived at said conclusion in the next section. However, I realized that I also didn't want this story to be about John going back for Elizabeth, actually finding her, and failing to bring her back. There were several reasons for my hesitation to write that type of story, and one reason was that if a successful rescue mission story would have been written out of denial for really happened to Elizabeth, then a straight-forward, failed rescue mission story would have been written to spite what failed to occur on-screen. As much as I criticized the producers and writers for failing to include something so crucial in order to respect their characters and said characters' defining attributes, I didn't want to disrespect the actual events that occurred before our eyes. Another reason that I didn't want a straight-forward, failed rescue mission was that if John and his team had actually found Elizabeth, then there would have been a number of continuity issues that would have needed to be addressed – for instance, they're bound to get captured and their minds probed, so how to explain why the Replicators don't go to attack Atlantis at the beginning of Season 4, because they've discovered Atlantis' new location? Or, in "This Mortal Coil," John obtains information that leads him to believe that Elizabeth had perished on the Replicator planet shortly after her capture, and it also seemed very clear that John never found Elizabeth – so how to explain his quiet remorse at the end of the episode, when he informed Rodney that he would be approving the removal of Elizabeth's personal items the next day, if he had actually found her during a failed rescue mission, because he might have then reacted more intensely. Because I wanted this story to be something that could have contributed to the existing episodes in Season 4, it was necessary for me to take all these canon events into consideration when writing this story._

 _Somewhere along the process of trying to respect on-screen events, I found myself thinking about the Replicators and their mind-probing, and we have seen on-screen a few times how deception has occurred due to mind-probing, and we don't know what's real and what is not. For the purposes of incorporating suspense, I began contemplating the thought that a portion of my story isn't actually happening, but rather only a scenario played out in John's mind. And I suddenly had the idea: what if the entire mission never really happened? What if, for some reason, John and his team never made it to the Replicator planet, John fell unconscious, and the entire mission happened only in John's mind? The moment that this idea occurred to me, I was both extremely excited and apprehensive about using it. It would have been the biggest plot twist in this story; I figured that readers might have been expecting some sort of deception on part of the Replicators' mind-probing, when ironically, the Replicators would have had nothing to do with the illusion of reality caused by a dream. Initially, I felt that it seemed like too extreme of a cop-out to avoid continuity issues between my story and the actual episodes, and I was on the fence about this idea for a very long time._

 _However, I finally decided to go for it, one reason being that I felt it was a brilliant way to explore a hypothetical way that a rescue mission for Elizabeth might have turned out without the events actually occurring, thus avoiding any continuity issues that might have resulted had John actually found Elizabeth. Additionally, this storytelling strategy allowed me to explore one of John's deepest fears about letting his people down and his consequential emotional reactions to his failures: in his dream, he becomes so desperate to bring Elizabeth back that he even shoots her just so he could carry her back to the Jumper himself, only in the end to have failed because Elizabeth refuses to leave… and when he wakes up, not only is he devastated because he failed to bring Elizabeth back in his dream, but his shock and grief turns even more potent when he realizes that the rescue mission never actually happened, and he had never found Elizabeth in the first place. Finally, I realized that making the rescue mission only a dream was the only way to honor the episodes as they were while doing justice to the John Sheppard we know and love who did everything he could to return for one of his people. What was most important was John's motives for going back for Elizabeth and his actions that were consistent with his core values, and in this story, he did just that. In the end, the mission failed… just not in the way we expected. And that is how we get the failed rescue mission that never happened that could have occurred in early Season 4._

* * *

 ** _"We don't leave our people behind": John Sheppard's fundamental belief_**

 _When I began writing this, I knew that I wanted the story to address one matter that I felt was a serious fault on part of the producers and writers, and that was the absence of an on-screen rescue mission to bring Elizabeth back. In "Reunion," we only see John Sheppard and Colonel Carter have a brief discussion about a possible rescue mission for Elizabeth before Carter dismisses John, and the topic is never once brought up again. The main issue, for me, wasn't that Elizabeth didn't come back, but rather that no noticeable attempts were made to bring her back. I thought that this was a serious mistake on part of the producers and writers, because one of John's defining character traits is his loyalty to his people, and if nothing happened that wasn't shown on-screen, then I honestly would have thought that John had displayed a major lack of integrity in this situation in not adhering to his deeply rooted belief in not leaving his people behind._

 _Now, could have John actually not done anything beyond his brief conversation with Colonel Carter? When I began writing this, I found myself mulling over one question repeatedly: did John go back for Elizabeth and failed, and we just didn't see it on-screen… or did he not? For a while, I entertained the notion that he never really went back, and I considered possible motives for his lack of action, because I believed that if he truly never returned for Elizabeth, then he must have had a very critical reason for not doing so. However, the more I thought about it, the more I began to believe that there was no way that he would have done absolutely nothing, simply because he has proved so many times on-screen that he doesn't leave his people behind: 1) Before he became involved in the Atlantis expedition, he was stationed in McMurdo because of his tarnished military record, and we see him in Season 3 disobeying direct orders and flying back to Afghanistan alone for one of his fellow comrades. 2) When Colonel Sumner and the Athosians were culled by the Wraith at the beginning of the expedition, he argued with Elizabeth that it was essential that he go back for them because they don't leave their people in the hands of the enemy. 3) After Lieutenant Ford became addicted to the Wraith enzyme and escaped Atlantis, John didn't give up on trying to bring him back, despite the reality that Ford was clearly not in the right state of mind… not when he encountered Ford on the planet where he met Ronon, and not when he became involved in Ford's plan to destroy a Wraith Hive ship later on in the season. 4) In Season 3, when Ronon was recaptured by the Wraith, John employed Colonel Caldwell and the Daedalus in order to rescue his friend on Sateda, even standing up to Caldwell when Caldwell expressed skepticism over the likelihood that the rescue mission would succeed. 5) Finally, when Teyla was kidnapped by Michael toward the end of Season 4, John relentlessly pursued her over the course of several episodes, depending on information from Carson Beckett's clone, despite Colonel Carter's hesitation, because it was the only lead he had – and later disregarding his personal injuries in "Search and Rescue," insisting to Jennifer Keller and Colonel Carter that he go on the mission to Michael's cruiser to rescue Teyla, even telling Colonel Carter, "I'll surrender for court martial when I'm done."_

 _Over and over, John has proved his loyalty to his people, and if there is any chance at all of saving them, then he refuses to give up. Elizabeth, therefore, should have been no exception, despite the reality that she could have been compromised and been a threat to the city… after all, John was willing to save Ford, who had already become dangerous when he threatened to kill people in Atlantis and stole a Jumper to escape the city, and who later became so addicted to the Wraith enzyme that he was no longer the happy-go-lucky Lieutenant that he once was. John wouldn't have not gone back for Elizabeth because of the possibility that she might be a threat to the city, and he wouldn't have not gone back for her even if Elizabeth explicitly told him not to herself, because it is his deeply rooted core belief that he doesn't leave his people behind._

 _As a result, I believed that John did go back for Elizabeth, and he would have done everything he could to get her back – and we just didn't see his rescue attempts on-screen. In Afghanistan, he wasn't afraid to disobey orders and go back alone for one man, and similarly, in this story, we see that he truly was ready to take off alone, against Colonel Carter and the IOA's orders, and he would do it even if he didn't have a plan, even if his teammates didn't go with him. Many times over, John has demonstrated that he doesn't leave his people behind, and he would return for them no matter the risks, no matter the costs, for Elizabeth and for anyone else. And in this story, he goes back for Elizabeth… and even though events didn't turn out as planned, the important thing is that he tried. He tried so hard, and his undying loyalty to his people is what we admire and respect him for, regardless of the final outcome._

* * *

 ** _The sympathy of a leader: Colonel Carter's arrival in Atlantis_**

 _Another issue that I wanted this story to address was the manner in which Colonel Carter was brought in as the new leader of Atlantis after "Lifeline." While I find Colonel Carter a good and respectable character, it hurt very much to see her brought on the show with Rodney acting as if nothing short of a tragedy had just happened, and it also hurt to see her not only refuse John's proposal to rescue Elizabeth, but also not even offer her assistance in planning a rescue mission – which I thought was out of character, considering that her intelligence and resourcefulness were on par with those of Rodney. I felt that the abrupt manner in which the producers introduced Colonel Carter to the show as well as their dismissal of the issue of Elizabeth's capture was extremely disrespectful, not only to the leader of Atlantis whom we had known and respected for three years, but also to Colonel Carter's character, who was in a position in which she could have helped but didn't on-screen. I believed that these crucial on-screen mistakes at the beginning of Season 4 were a great injustice to both female characters, and they left a bad taste in my mouth and made it very difficult for me to watch the entire season._

 _When I began writing this story, I realized that I would have been able to better accept Colonel Carter's entrance into the show had Colonel Carter addressed Elizabeth's capture on the Replicator planet more than what was shown on-screen, and I would have also appreciated her expressing more sympathy to John and his team for what they were going through emotionally in regards to Elizabeth's unknown fate. As a result, I attempted to rectify this on-screen shortcoming with a scene between John and Colonel Carter a few days after the failed rescue mission, and I hope that it came across as realistic and believable. Based on Colonel Carter's appearances in SGA and in a few episodes of SG-1 that I have watched, I feel that I can surmise that she is an intelligent and compassionate leader who respects the rules of the military while is also capable of looking at the larger picture in any given situation. She also isn't afraid of admitting her own mistakes, and she can understand people's underlying motives for their actions and sympathize with those who have experienced a tremendous loss. I feel that seeing Colonel Carter showcase her compassion and sympathy as well as acknowledge personal faults in this story has consequently allowed me to better accept her role in Season 4 of SGA, and I hope that I have done justice to her character in this story._

* * *

 ** _An unpaid debt: John Sheppard's indebtedness to Elizabeth Weir_**

 _This story was very much meant to be character-driven, and many of my aforementioned goals when writing this story had to do with respecting my characters and their individual traits and personal beliefs. While John enjoyed a number of memorable character moments on the show, a final goal of mine for this story was to highlight John's emotions and to acknowledge numerous aspects of his character development. I had already emphasized John's loyalty to his people as one of his key character traits; no matter whom he had left behind on the Replicator planet, he would have done everything he could to return for them. However, I thought it crucial that the reality was that Elizabeth was the one who had been left behind, and even though his emotional reaction toward Elizabeth's fate wasn't especially fleshed out on-screen, in this story, we see him expressing emotions that he may have been suppressing all that time: an exceptionally strong desire to return for Elizabeth; an intense frustration on the Replicator planet from Elizabeth's unwillingness to return to Atlantis; and finally a fierce grief in being unable to bring her back. When writing his dialogue with Elizabeth and depicting his internal feelings, I kept in mind major aspects of his character development over the course of the show and the unique relationship he had with Elizabeth. I believed that in this story, he would have experienced great emotional turmoil in regards to Elizabeth's loss – and I believe that he continued to mourn throughout Seasons 4 and 5 – and the reason that I believe that his emotional turmoil would have been exceptionally potent is that he feels remarkably indebted to Elizabeth for the profound impact that she has had on his life._

 _As John tells Teyla in this story, before he became involved in the Atlantis expedition, he was "just a damn Major who didn't know what the hell he was doing with his life." His military record was tarnished, and even though he very likely didn't regret his actions back in Afghanistan, he had to face the consequences of disobeying direct orders, and his life and future seemed bleak in McMurdo. Then he found out about the SGC and met Elizabeth, and at first glance, it would appear that she wanted him on the Atlantis expedition only because he had the Ancient gene. However, she was aware of John's questionable behavior in Afghanistan, and she was undoubtedly an intelligent enough woman to recognize that John's tendency to not follow the chain of command might prove hazardous on the expedition – yet, it would appear that she looked past that when she spoke with General O'Neill in Antarctica and emphasized that John had been trying to save the lives of three servicemen. I believe that Elizabeth saw something in John's disreputable record that she admired or at the very least considered an asset, and she wanted John on the expedition not only in spite of his past actions, but perhaps because of them._

 _Of course, John probably didn't know what he was getting himself into when he first stepped through the Stargate. But over the following several years, his life changed completely. It might have been a twist of fate that Colonel Sumner perished so early in the expedition, but after John was forced into the position of ranking military officer, he received the opportunity to make an incredible impact on the lives of the city's inhabitants as well as those living in the Pegasus Galaxy, protecting those in danger who couldn't help themselves. Over the years, he formed close bonds with his off-world team as well as Carson and Elizabeth, even confiding in Teyla in "Sateda" that she, Elizabeth, Ronon, Carson, and Rodney were the closest thing he had to a family… and for a man who felt that he was leaving nothing behind when he left Earth, the relationships that he found in Atlantis clearly meant a great deal to him. After the expedition's first year, John was also promoted to Lieutenant Colonel after Elizabeth insisted to the SGC back on Earth that he remain ranking military officer in Atlantis. He told Elizabeth in "Intruder," "There's a lot of people in the Air Force who never thought I'd make it past Captain," and it's clear that his unexpected promotion was very much Elizabeth's doing. Even though Elizabeth and John had their disagreements during the first year – most notably their contention during the alien nanovirus infection, when John challenged Elizabeth's authority – Elizabeth was willing to acknowledge, to a certain extent, that the ends justified the means, and she recognized John's value to the expedition and unflinchingly supported him against those who wished to replace him._

 _Had Elizabeth never asked John to join the expedition, none of this would have happened. John might still be in McMurdo or stationed in another remote location, unable to make an impact on the lives of others as he so fiercely desires. He was divorced back on Earth and estranged from his father and brother, and there seemed to be very few people in his life on whom he could depend for professional and personal support. It was only because Elizabeth looked past his disgraced surface, not only giving him a second chance during a time when it seemed as if he had nothing left to lose, but also continuing to stalwartly support him during the first few years of the expedition against those who didn't express considerable faith in him, that John recognized his self-worth, obtained an opportunity to make a profound impact on the lives of others, and gained invaluable relationships to support him when facing life and death._

 _As a result, I believe that John felt an incredible sense of indebtedness toward Elizabeth on a very personal level, which is why in this story, he becomes increasingly persistent in finding her and bringing her back. As I contemplated what might have triggered John to become so resolutely determined to go back for her, I considered Elizabeth's conversation with Teyla in "First Strike" about how she was considering stepping down because she felt that her services were no longer respected. This scene was clearly foreshadowing Elizabeth's fate of being captured by the Replicators, and I wondered how John would have reacted had he known that Elizabeth was considering resigning before the Replicator attack. Seeing as he was aware of the politics and red tape with which she had to deal with the IOA and that people had questioned her decisions in Atlantis – just as his own past actions had been questioned on Earth – I believed that John would have reacted very intensely upon learning that, in a very cruel twist of fate, the IOA and Earth's military had gotten what they wanted. He would have done anything he could to bring her back, not only because of his "we don't leave our people behind" mantra, but also to repay Elizabeth for everything that she had done for him and he now was determined to do for her. I hope that I have done John Sheppard's character justice in portraying his humanity and emotions, in addition to making this a story about a man who fiercely desires to repay a debt to someone who changed his life for the better._

 _(And of course, one could also argue that John was incredibly determined to bring Elizabeth back because he had unresolved feelings for Elizabeth. I think that this was definitely a possibility, and it's a very believable factor that could have compounded to his grief toward losing her, and since I ship Sparky myself, I won't dispute this claim. :)_

* * *

 ** _Forward and onward: Conclusion_**

 _I began writing this story because I was, in any sense of the definition, in a state of mourning. It feels unusual to me that nine years after Elizabeth was gone from Atlantis and seven years after SGA was cancelled, the show and its characters continue to affect me on a very personal level, and I think that I needed to write this in order to fully accept what happened and move forward from the past. I had many conflicting feelings toward an incredible show whose run was tragically cut short after only five years, and I sympathized with its beautiful, complex characters who were never always done the greatest justice by the producers and writers. In the end, I needed, at the very least, to reconcile my internal feelings in order to let go of a long-lasting grief and finally accept and appreciate all the seasons for what they were._

 _Writing this story was an incredible journey for me, and I'm actually sad now that it's completed. This story took me only two weeks to write, but then again, I'm out of school for the summer and have had quite a lot of time to involve myself in the SGA fandom again and work on personal projects. To be honest, I began this story thinking that it would be a one-shot, a few thousand words at most, and I hadn't known that it would turn out to be a multi-chapter story, nearly 20,000 words long, and something that I would personally place into my own head canon – and then I surprised myself by writing a 4,700-word long essay detailing my entire writing process, which was a signal to me that I had subconsciously put a lot of thought into every detail of this story. I look back to my earliest ventures into fanfiction three or four years ago, and I feel like my writing has matured greatly in terms of quality, characterization, and complexity of plot, and I've also become much more confident with my writing. I would never have thought three or four years ago that I would write this one day, but now that I have, it makes me hopeful for future stories that I may tackle in the years to come._

 _(Edited July 2017) I wanted to say thank you to everyone who has read through this story as well as left reviews. To those of you who have left guest reviews on this story, as well as others of mine, know that I wish I could reply to them. I'm grateful that there are still people out there who are involved in the fandom and with whom I can share my work, and it means a lot when people take the time to share their thoughts about the show and my work with me. Not only does feedback encourage me to keep writing on my radar and set goals for future projects, but with this story in particular, it also makes me feel that after all that was unfortunate on the show, I have done something good in writing this story. If anything, I hope that this story has provided all of us with a bit of closure as well as brought us all a little closer together. What happened to our beloved characters and actors was nothing short of unjust, and I hope that this story has helped us viewers and readers realize that we are not alone in our anger and grief at what happened to our characters, as well as their stories that haven't been completed yet._


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